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HEADER HYDROLASE 09-JAN-97 1CVL
TITLE CRYSTAL STRUCTURE OF BACTERIAL LIPASE FROM CHROMOBACTERIUM
TITLE 2 VISCOSUM ATCC 6918
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRIACYLGLYCEROL HYDROLASE;
COMPND 3 CHAIN: NULL;
COMPND 4 EC: 3.1.1.3;
COMPND 5 OTHER_DETAILS: CHAIN BREAK FROM V 220 - G 222
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: CHROMOBACTERIUM VISCOSUM;
SOURCE 3 ATCC: 6918
KEYWDS TRIACYLGLYCEROL-HYDROLASE, X-RAY CRYSTALLOGRAPHY,
KEYWDS 2 PSEUDOMONADACEAE, OXYANION, CIS-PEPTIDE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR D.A.LANG,B.HOFMANN,L.HAALCK,H.-J.HECHT,F.SPENER,
AUTHOR 2 R.D.SCHMID,D.SCHOMBURG
REVDAT 1 01-APR-97 1CVL 0
JRNL AUTH D.LANG,B.HOFMANN,L.HAALCK,H.J.HECHT,F.SPENER,
JRNL AUTH 2 R.D.SCHMID,D.SCHOMBURG
JRNL TITL CRYSTAL STRUCTURE OF A BACTERIAL LIPASE FROM
JRNL TITL 2 CHROMOBACTERIUM VISCOSUM ATCC 6918 REFINED AT 1.6
JRNL TITL 3 ANGSTROMS RESOLUTION
JRNL REF J.MOL.BIOL. V. 259 704 1996
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.6 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROLSQ
REMARK 3 AUTHORS : KONNERT,HENDRICKSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.6
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : 88.
REMARK 3 NUMBER OF REFLECTIONS : 32395
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : RANDOM
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.178
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 32395
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2316
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 230
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.9
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18
REMARK 3 ESD FROM SIGMAA (A) : 0.18
REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.0
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.021 ; 0.020
REMARK 3 ANGLE DISTANCE (A) : 0.044 ; 0.040
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.054 ; 0.050
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.015 ; 0.020
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.082 ; 0.075
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : 0.169 ; 0.300
REMARK 3 MULTIPLE TORSION (A) : 0.212 ; 0.300
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : 2.704 ; 3.000
REMARK 3 STAGGERED (DEGREES) : 13.070; 15.000
REMARK 3 TRANSVERSE (DEGREES) : 25.00 ; 20.00
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.300 ; 1.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.05 ; 1.50
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.64 ; 1.00
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.26 ; 1.5
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE DISORDERED REGION (VAL 220, LEU 221 AND GLY 223) WAS
REMARK 3 NOT MODELED OR REFINED.
REMARK 4
REMARK 4 1CVL COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6
REMARK 6 PARTLY DEGRADED LIPASE AS A RESULT OF UNSPECIFIC
REMARK 6 PROTEOLYTIC DIGESTION DURING PURIFICATION AND/OR STORAGE
REMARK 6 PROVEN BY MALDI-TOF MASS SPECTROSCOPY
REMARK 6 MOLECULAR WEIGHT: CALCULATED -- 33091 DALTON
REMARK 6 MEASURED -- 32839 DALTON
REMARK 7
REMARK 7 LEU 17 AND THR 20 ARE RESIDUES LOCATED ON THE OXYANION
REMARK 7 LOOP, A STRUCTURAL MOTIF, WHICH IS IMPORTANT FOR THE
REMARK 7 STABILIZATION OF THE NEGATIVE CHARGE OF THE TETRAHEDRAL
REMARK 7 INTERMEDIATE DURING ENZYME CATALYSIS. THEY POSSESS AN
REMARK 7 ENERGETICALLY HIGHER CONFORMATION ACTIVE SITE SER 87 HAS
REMARK 7 THE TYPICAL CONFORMATION FOR THE NUCLEOPHILE OF A
REMARK 7 ALPHA/BETA HYDROLASE FOLD ENZYME.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NOV-1993
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 6.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : BW6
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : CCP4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33644
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.6
REMARK 200 RESOLUTION RANGE LOW (A) : 20.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 88.
REMARK 200 DATA REDUNDANCY : 2.6
REMARK 200 R MERGE (I) : 0.053
REMARK 200 R SYM (I) : 0.053
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64
REMARK 200 COMPLETENESS FOR SHELL (%) : 73.7
REMARK 200 DATA REDUNDANCY IN SHELL : 1.2
REMARK 200 R MERGE FOR SHELL (I) : 0.053
REMARK 200 R SYM FOR SHELL (I) : 0.22
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.1
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR
REMARK 200 SOFTWARE USED: MLPHARE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM
REMARK 280 10-14 % PEG 4000, 10-14 % MPD, 100 MM CITRATE/PHOSPHATE
REMARK 280 BUFFER, PH 6.4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 1/2-X,1/2+Y,-Z
REMARK 290 4555 1/2+X,1/2-Y,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 20.53979
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 78.40678
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.53979
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 78.40678
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. SOME OF THESE MAY BE ATOMS
REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL. ATOMS WITH
REMARK 500 NON-BLANK ALTERNATE LOCATION INDICATORS ARE NOT INCLUDED
REMARK 500 IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH 618 O HOH 542 1554 0.73
REMARK 500 O HOH 542 O HOH 618 1556 0.73
REMARK 500 O HOH 600 O HOH 540 4556 1.98
REMARK 500 O HOH 540 O HOH 600 4456 1.98
REMARK 700
REMARK 700 SHEET
REMARK 700 THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. A
REMARK 700 BIFURCATED SHEET IS REPRESENTED BY TWO SHEETS WHICH HAVE
REMARK 700 ONE OR MORE IDENTICAL STRANDS. SHEETS A1 AND A2 REPRESENT
REMARK 700 ONE BIFURCATED SHEET.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CA
REMARK 800 SITE_DESCRIPTION: CA BINDING SITE.
REMARK 800
REMARK 800 SITE_IDENTIFIER: ACT
REMARK 800 SITE_DESCRIPTION: THE CATALYTIC TRIAD OF THE ACTIVE
REMARK 800 CENTER CONSISTS OF THE RESIDUES SER 87 - HIS 285 - ASP
REMARK 800 263, ALTHOUGH THEY ARE NOT EXPOSED TO THE SOLVENT, BUT A
REMARK 800 NARROW CHANNEL CONNECTS THEM WITH THE SURFACE.
REMARK 800
REMARK 800 SITE_IDENTIFIER: OXY
REMARK 800 SITE_DESCRIPTION: PERFORMED OXYANION, STABILIZED BY THE
REMARK 800 AMIDE NITROGEN ATOMS OF LEU 17 AND GLN 88, ALREADY
REMARK 800 PRESENT IN CLOSED CONFORMATION OF THE LIPASE.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 1CVL SWS Q05489 1 - 39 NOT IN ATOMS LIST
REMARK 999
REMARK 999 REFERENCE: THE SEQUENCE FOR PSEUDOMONAS GLUMAE DESCRIBED
REMARK 999 IN FRENKEN ET AL. (1992), APPL. ENVIR. MICROBIOL. 58
REMARK 999 3787-3791; IS IDENTICAL TO THE AMINO ACID SEQUENCE OF
REMARK 999 CHROMOBACTERIUM VISCOSUM DESCRIBED IN SHIZUOKA ET AL.,
REMARK 999 1989 (GERMAN PATENT 3908131 A1).
DBREF 1CVL 1 219 SWS Q05489 LIP_PSEGL 40 258
DBREF 1CVL 223 319 SWS Q05489 LIP_PSEGL 259 358
SEQADV 1CVL SWS Q05489 LEU 260 GAP IN PDB ENTRY
SEQADV 1CVL SWS Q05489 GLY 261 GAP IN PDB ENTRY
SEQADV 1CVL SWS Q05489 VAL 262 GAP IN PDB ENTRY
SEQRES 1 319 ALA ASP THR TYR ALA ALA THR ARG TYR PRO VAL ILE LEU
SEQRES 2 319 VAL HIS GLY LEU ALA GLY THR ASP LYS PHE ALA ASN VAL
SEQRES 3 319 VAL ASP TYR TRP TYR GLY ILE GLN SER ASP LEU GLN SER
SEQRES 4 319 HIS GLY ALA LYS VAL TYR VAL ALA ASN LEU SER GLY PHE
SEQRES 5 319 GLN SER ASP ASP GLY PRO ASN GLY ARG GLY GLU GLN LEU
SEQRES 6 319 LEU ALA TYR VAL LYS GLN VAL LEU ALA ALA THR GLY ALA
SEQRES 7 319 THR LYS VAL ASN LEU ILE GLY HIS SER GLN GLY GLY LEU
SEQRES 8 319 THR SER ARG TYR VAL ALA ALA VAL ALA PRO GLN LEU VAL
SEQRES 9 319 ALA SER VAL THR THR ILE GLY THR PRO HIS ARG GLY SER
SEQRES 10 319 GLU PHE ALA ASP PHE VAL GLN ASP VAL LEU LYS THR ASP
SEQRES 11 319 PRO THR GLY LEU SER SER THR VAL ILE ALA ALA PHE VAL
SEQRES 12 319 ASN VAL PHE GLY THR LEU VAL SER SER SER HIS ASN THR
SEQRES 13 319 ASP GLN ASP ALA LEU ALA ALA LEU ARG THR LEU THR THR
SEQRES 14 319 ALA GLN THR ALA THR TYR ASN ARG ASN PHE PRO SER ALA
SEQRES 15 319 GLY LEU GLY ALA PRO GLY SER CYS GLN THR GLY ALA ALA
SEQRES 16 319 THR GLU THR VAL GLY GLY SER GLN HIS LEU LEU TYR SER
SEQRES 17 319 TRP GLY GLY THR ALA ILE GLN PRO THR SER THR VAL LEU
SEQRES 18 319 GLY VAL THR GLY ALA THR ASP THR SER THR GLY THR LEU
SEQRES 19 319 ASP VAL ALA ASN VAL THR ASP PRO SER THR LEU ALA LEU
SEQRES 20 319 LEU ALA THR GLY ALA VAL MET ILE ASN ARG ALA SER GLY
SEQRES 21 319 GLN ASN ASP GLY LEU VAL SER ARG CYS SER SER LEU PHE
SEQRES 22 319 GLY GLN VAL ILE SER THR SER TYR HIS TRP ASN HIS LEU
SEQRES 23 319 ASP GLU ILE ASN GLN LEU LEU GLY VAL ARG GLY ALA ASN
SEQRES 24 319 ALA GLU ASP PRO VAL ALA VAL ILE ARG THR HIS VAL ASN
SEQRES 25 319 ARG LEU LYS LEU GLN GLY VAL
HET CA 320 1
HETNAM CA CALCIUM ION
FORMUL 2 CA CA1 2+
FORMUL 3 HOH *230(H2 O1)
HELIX 1 1 ILE 33 SER 39 1 7
HELIX 2 2 ARG 61 THR 76 1 16
HELIX 3 3 GLY 89 VAL 99 5 11
HELIX 4 4 GLU 118 LEU 127 1 10
HELIX 5 5 THR 137 LEU 149 1 13
HELIX 6 6 THR 156 ALA 162 1 7
HELIX 7 7 THR 169 ASN 178 1 10
HELIX 8 8 ALA 237 THR 240 5 4
HELIX 9 9 SER 243 ASN 256 1 14
HELIX 10 10 ARG 268 SER 271 1 4
HELIX 11 11 PRO 303 LEU 316 1 14
SHEET 1 A1 6 VAL 44 VAL 46 0
SHEET 2 A1 6 VAL 11 VAL 14 1 N VAL 11 O TYR 45
SHEET 3 A1 6 VAL 81 HIS 86 1 N ASN 82 O PRO 10
SHEET 4 A1 6 VAL 104 ILE 110 1 N ALA 105 O VAL 81
SHEET 5 A1 6 SER 202 GLY 211 1 N LEU 205 O VAL 107
SHEET 6 A1 6 THR 196 VAL 199 -1 N VAL 199 O SER 202
SHEET 1 A2 6 VAL 44 VAL 46 0
SHEET 2 A2 6 PRO 10 VAL 14 1 N VAL 11 O TYR 45
SHEET 3 A2 6 VAL 81 HIS 86 1 N ASN 82 O PRO 10
SHEET 4 A2 6 VAL 104 ILE 110 1 N ALA 105 O VAL 81
SHEET 5 A2 6 SER 202 GLY 211 1 N LEU 205 O VAL 107
SHEET 6 A2 6 GLN 275 TYR 281 1 N SER 278 O GLY 210
SHEET 1 B 2 LYS 22 PHE 23 0
SHEET 2 B 2 VAL 27 ASP 28 -1 N VAL 27 O PHE 23
SHEET 1 C 2 ILE 214 PRO 216 0
SHEET 2 C 2 ALA 226 ASP 228 -1 N THR 227 O GLN 215
SSBOND 1 CYS 190 CYS 269
LINK CA CA 320 OD2 ASP 241
LINK CA CA 320 O GLN 291
CISPEP 1 GLN 291 LEU 292 0 -5.87
SITE 1 CA 6 ASP 241 ASP 287 GLN 291 VAL 295
SITE 2 CA 6 HOH 460 HOH 555
SITE 1 ACT 3 SER 87 HIS 285 ASP 263
SITE 1 OXY 2 LEU 17 GLN 88
CRYST1 41.080 156.820 43.610 90.00 90.00 90.00 P 21 21 2 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.024343 0.000000 0.000000 0.00000
SCALE2 0.000000 0.006377 0.000000 0.00000
SCALE3 0.000000 0.000000 0.022931 0.00000 |