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HEADER HYDROLASE 15-SEP-98 1BU8
TITLE RAT PANCREATIC LIPASE RELATED PROTEIN 2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PANCREATIC LIPASE RELATED PROTEIN 2;
COMPND 3 CHAIN: NULL;
COMPND 4 EC: 3.1.1.3;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS;
SOURCE 3 ORGANISM_COMMON: RAT;
SOURCE 4 ORGAN: PANCREAS;
SOURCE 5 SECRETION: PANCREATIC JUICE;
SOURCE 6 EXPRESSION_SYSTEM: INSECT CELL (SF9);
SOURCE 7 EXPRESSION_SYSTEM_VECTOR: BACULOVIRUS
KEYWDS HYDROLASE, LIPID DEGRADATION, PANCREATIC LIPASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.ROUSSEL,C.CAMBILLAU
REVDAT 1 23-DEC-98 1BU8 0
JRNL AUTH A.ROUSSEL,Y.YANG,F.FERRATO,R.VERGER,C.CAMBILLAU,
JRNL AUTH 2 M.LOWE
JRNL TITL STRUCTURE AND ACTIVITY OF RAT PANCREATIC LIPASE
JRNL TITL 2 RELATED PROTEIN 2
JRNL REF TO BE PUBLISHED
JRNL REFN 9999
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.8 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.843
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.8
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 750
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 50
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3
REMARK 3 NUMBER OF REFLECTIONS : 36060
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NONE
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.244
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.
REMARK 3 FREE R VALUE TEST SET COUNT : 1626
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 10
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.9
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 792
REMARK 3 BIN R VALUE (WORKING SET) : 0.1774
REMARK 3 BIN FREE R VALUE : 0.2763
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3518
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 15
REMARK 3 SOLVENT ATOMS : 327
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.78
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) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.4
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.5
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.3
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PARAM19X.PRO
REMARK 3 PARAMETER FILE 2 : PARHCSDX.PRO
REMARK 3 PARAMETER FILE 3 : PARAM3_MOD.CHO
REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO
REMARK 3 TOPOLOGY FILE 2 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 3 : TOPH3.CHO
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1BU8 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 5
REMARK 5 WARNING
REMARK 5 1BU8: THIS IS LAYER 1 RELEASE.
REMARK 5
REMARK 5 PLEASE NOTE THAT THIS ENTRY WAS RELEASED AFTER DEPOSITOR
REMARK 5 CHECKING AND APPROVAL BUT WITHOUT PDB STAFF INTERVENTION.
REMARK 5 AN AUXILIARY FILE, AUX1BU8.RPT, IS AVAILABLE FROM THE
REMARK 5 PDB FTP SERVER AND IS ACCESSIBLE THROUGH THE 3DB BROWSER.
REMARK 5 THE FILE CONTAINS THE OUTPUT OF THE PROGRAM WHAT_CHECK AND
REMARK 5 OTHER DIAGNOSTICS.
REMARK 5
REMARK 5 NOMENCLATURE IN THIS ENTRY, INCLUDING HET RESIDUE NAMES
REMARK 5 AND HET ATOM NAMES, HAS NOT BEEN STANDARDIZED BY THE PDB
REMARK 5 PROCESSING STAFF. A LAYER 2 ENTRY WILL BE RELEASED SHORTLY
REMARK 5 AFTER THIS STANDARDIZATION IS COMPLETED AND APPROVED BY THE
REMARK 5 DEPOSITOR. THE LAYER 2 ENTRY WILL BE TREATED AS A
REMARK 5 CORRECTION TO THIS ONE, WITH THE APPROPRIATE REVDAT RECORD.
REMARK 5
REMARK 5 FURTHER INFORMATION INCLUDING VALIDATION CRITERIA USED IN
REMARK 5 CHECKING THIS ENTRY AND A LIST OF MANDATORY DATA FIELDS
REMARK 5 ARE AVAILABLE FROM THE PDB WEB SITE AT
REMARK 5 HTTP://WWW.PDB.BNL.GOV/.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : SEP-1997
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : LURE
REMARK 200 BEAMLINE : W32
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97
REMARK 200 MONOCHROMATOR : LURE MIRRORS
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47899
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.8
REMARK 200 RESOLUTION RANGE LOW (A) : 10.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.5
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5
REMARK 200 DATA REDUNDANCY : 2.4
REMARK 200 R MERGE (I) : 0.063
REMARK 200 R SYM (I) : 0.063
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.8
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83
REMARK 200 COMPLETENESS FOR SHELL (%) : 81.9
REMARK 200 DATA REDUNDANCY IN SHELL : 2.2
REMARK 200 R MERGE FOR SHELL (I) : 0.420
REMARK 200 R SYM FOR SHELL (I) : 0.420
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.3
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 1THG
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS:
REMARK 280 PROTEIN WAS CRYSTALLIZED FROM
REMARK 280 8% PEG 8000 WITH 0.1 M TRIS/HCL PH 8.4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-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 39.56635
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 LYS 405 TO PHE 410
DBREF 1BU8 1 449 SWS P54318 LIP2_RAT 17 468
SEQADV 1BU8 ALA 244 SWS P54318 THR 261 CONFLICT
SEQADV 1BU8 ALA 404 SWS P54318 ASN 422 CONFLICT
SEQADV 1BU8 ALA 404 SWS P54318 LYS 423 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 404 SWS P54318 VAL 424 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 404 SWS P54318 ILE 425 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 404 SWS P54318 ASN 426 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 404 SWS P54318 LEU 427 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 404 SWS P54318 PHE 428 GAP IN PDB ENTRY
SEQADV 1BU8 ALA 412 SWS P54318 ARG 429 CONFLICT
SEQRES 1 452 LYS GLU VAL CYS TYR GLY HIS LEU GLY CYS PHE SER ASN
SEQRES 2 452 ASP LYS PRO TRP ALA GLY MET LEU GLN ARG PRO LEU LYS
SEQRES 3 452 ILE PHE PRO TRP SER PRO GLU ASP ILE ASP THR ARG PHE
SEQRES 4 452 LEU LEU TYR THR ASN GLU ASN PRO ASN ASN TYR GLN LYS
SEQRES 5 452 ILE SER ALA THR GLU PRO ASP THR ILE LYS PHE SER ASN
SEQRES 6 452 PHE GLN LEU ASP ARG LYS THR ARG PHE ILE VAL HIS GLY
SEQRES 7 452 PHE ILE ASP LYS GLY GLU ASP GLY TRP LEU LEU ASP MET
SEQRES 8 452 CYS LYS LYS MET PHE GLN VAL GLU LYS VAL ASN CYS ILE
SEQRES 9 452 CYS VAL ASP TRP ARG ARG GLY SER ARG THR GLU TYR THR
SEQRES 10 452 GLN ALA SER TYR ASN THR ARG VAL VAL GLY ALA GLU ILE
SEQRES 11 452 ALA PHE LEU VAL GLN VAL LEU SER THR GLU MET GLY TYR
SEQRES 12 452 SER PRO GLU ASN VAL HIS LEU ILE GLY HIS SER LEU GLY
SEQRES 13 452 ALA HIS VAL VAL GLY GLU ALA GLY ARG ARG LEU GLU GLY
SEQRES 14 452 HIS VAL GLY ARG ILE THR GLY LEU ASP PRO ALA GLU PRO
SEQRES 15 452 CYS PHE GLN GLY LEU PRO GLU GLU VAL ARG LEU ASP PRO
SEQRES 16 452 SER ASP ALA MET PHE VAL ASP VAL ILE HIS THR ASP SER
SEQRES 17 452 ALA PRO ILE ILE PRO TYR LEU GLY PHE GLY MET SER GLN
SEQRES 18 452 LYS VAL GLY HIS LEU ASP PHE PHE PRO ASN GLY GLY LYS
SEQRES 19 452 GLU MET PRO GLY CYS GLN LYS ASN ILE LEU SER THR ILE
SEQRES 20 452 VAL ASP ILE ASN GLY ILE TRP GLU GLY THR GLN ASN PHE
SEQRES 21 452 VAL ALA CYS ASN HIS LEU ARG SER TYR LYS TYR TYR ALA
SEQRES 22 452 SER SER ILE LEU ASN PRO ASP GLY PHE LEU GLY TYR PRO
SEQRES 23 452 CYS SER SER TYR GLU LYS PHE GLN GLN ASN ASP CYS PHE
SEQRES 24 452 PRO CYS PRO GLU GLU GLY CYS PRO LYS MET GLY HIS TYR
SEQRES 25 452 ALA ASP GLN PHE GLU GLY LYS THR ALA THR VAL GLU GLN
SEQRES 26 452 THR VAL TYR LEU ASN THR GLY ASP SER GLY ASN PHE THR
SEQRES 27 452 ARG TRP ARG TYR LYS VAL SER VAL THR LEU SER GLY ALA
SEQRES 28 452 LYS LYS LEU SER GLY TYR ILE LEU VAL ALA LEU TYR GLY
SEQRES 29 452 ASN ASN GLY ASN SER LYS GLN TYR GLU ILE PHE LYS GLY
SEQRES 30 452 SER LEU LYS PRO GLU ALA ARG HIS VAL ARG ASP ILE ASP
SEQRES 31 452 VAL ASP ILE ASN VAL GLY GLU ILE GLN LYS VAL LYS PHE
SEQRES 32 452 LEU TRP ASN ASN LYS VAL ILE ASN LEU PHE ARG PRO THR
SEQRES 33 452 LEU GLY ALA SER GLN ILE THR VAL GLN SER GLY VAL ASP
SEQRES 34 452 GLY LYS GLU TYR ASN PHE CYS SER SER ASP THR VAL ARG
SEQRES 35 452 GLU ASP VAL LEU GLN SER LEU TYR PRO CYS
HET NAG 451 0
HETNAM NAG N-ACETYL-D-GLUCOSAMINE
FORMUL 2 NAG C8 H15 N1 O6
FORMUL 3 HOH *295(H2 O1)
HELIX 1 1 GLY 6 LEU 8 5 3
HELIX 2 2 PRO 31 ILE 34 1 4
HELIX 3 3 PRO 56 LYS 60 5 5
HELIX 4 4 ASP 83 GLN 95 5 13
HELIX 5 5 ARG 107 SER 110 1 4
HELIX 6 6 TYR 114 MET 139 1 26
HELIX 7 7 PRO 143 ASN 145 5 3
HELIX 8 8 SER 152 ARG 164 5 13
HELIX 9 9 GLU 187 VAL 189 5 3
HELIX 10 10 PRO 193 ASP 195 5 3
HELIX 11 11 ILE 209 TYR 212 1 4
HELIX 12 12 PRO 228 GLY 230 5 3
HELIX 13 13 ILE 248 TRP 252 1 5
HELIX 14 14 CYS 261 LEU 275 1 15
HELIX 15 15 PRO 277 GLY 279 5 3
HELIX 16 16 TYR 288 GLN 293 1 6
HELIX 17 17 HIS 309 GLN 313 5 5
SHEET 1 A 2 GLU 2 CYS 4 0
SHEET 2 A 2 CYS 10 SER 12 -1 N PHE 11 O VAL 3
SHEET 1 B 9 GLN 50 ILE 52 0
SHEET 2 B 9 ARG 37 THR 42 -1 N LEU 40 O GLN 50
SHEET 3 B 9 VAL 99 ASP 105 -1 N ASP 105 O ARG 37
SHEET 4 B 9 LYS 69 VAL 74 1 N LYS 69 O ASN 100
SHEET 5 B 9 VAL 146 HIS 151 1 N HIS 147 O THR 70
SHEET 6 B 9 ARG 171 LEU 175 1 N ARG 171 O LEU 148
SHEET 7 B 9 VAL 199 ILE 202 1 N ASP 200 O ILE 172
SHEET 8 B 9 LEU 224 PRO 228 1 N LEU 224 O VAL 201
SHEET 9 B 9 GLN 323 LEU 327 1 N GLN 323 O ASP 225
SHEET 1 C 4 ARG 381 VAL 388 0
SHEET 2 C 4 TRP 338 SER 347 -1 N VAL 344 O HIS 382
SHEET 3 C 4 GLY 416 SER 424 -1 N GLN 423 O LYS 341
SHEET 4 C 4 GLU 429 CYS 433 -1 N PHE 432 O ILE 420
SHEET 1 D 4 GLN 444 TYR 447 0
SHEET 2 D 4 ILE 395 ASN 403 -1 N PHE 400 O GLN 444
SHEET 3 D 4 LEU 351 GLY 361 -1 N TYR 360 O GLN 396
SHEET 4 D 4 TYR 369 LEU 376 -1 N LEU 376 O LEU 351
SSBOND 1 CYS 4 CYS 10
SSBOND 2 CYS 90 CYS 101
SSBOND 3 CYS 237 CYS 261
SSBOND 4 CYS 285 CYS 296
SSBOND 5 CYS 299 CYS 304
SSBOND 6 CYS 433 CYS 449
LINK C1 NAG 451 ND2 ASN 334
CISPEP 1 LYS 15 PRO 16 0 0.39
CISPEP 2 ILE 210 PRO 211 0 1.07
CRYST1 57.393 79.133 60.940 90.00 102.07 90.00 P 1 21 1 2
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 0.017424 0.000000 0.003727 0.00000
SCALE2 0.000000 0.012637 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016781 0.00000 |