HEADER HYDROLASE 02-APR-04 1V0W
TITLE PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE
TITLE 2 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOSPHOLIPASE D;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.1.4.4
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.;
SOURCE 3 ORGANISM_TAXID: 172564;
SOURCE 4 STRAIN: PMF
KEYWDS PHOSPHOLIPASE D, HYDROLASE, SUBSTRATE SOAK,
KEYWDS 2 DIBUTYRYLPHOSPHATIDYLCHOLINE, DIC4PC
EXPDTA X-RAY DIFFRACTION
AUTHOR I.LEIROS,S.MCSWEENEY,E.HOUGH
REVDAT 3 13-DEC-23 1V0W 1 LINK
REVDAT 2 24-FEB-09 1V0W 1 VERSN
REVDAT 1 03-JUN-04 1V0W 0
JRNL AUTH I.LEIROS,S.MCSWEENEY,E.HOUGH
JRNL TITL THE REACTION MECHANISM OF PHOSPHOLIPASE D FROM STREPTOMYCES
JRNL TITL 2 SP. STRAIN PMF. SNAPSHOTS ALONG THE REACTION PATHWAY REVEAL
JRNL TITL 3 A PENTACOORDINATE REACTION INTERMEDIATE AND AN UNEXPECTED
JRNL TITL 4 FINAL PRODUCT
JRNL REF J.MOL.BIOL. V. 339 805 2004
JRNL REFN ISSN 0022-2836
JRNL PMID 15165852
JRNL DOI 10.1016/J.JMB.2004.04.003
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH I.LEIROS,F.SECUNDO,C.ZAMBONELLI,S.SERVI,E.HOUGH
REMARK 1 TITL THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D
REMARK 1 REF STRUCTURE V. 8 655 2000
REMARK 1 REFN ISSN 0969-2126
REMARK 1 PMID 10873862
REMARK 1 DOI 10.1016/S0969-2126(00)00150-7
REMARK 2
REMARK 2 RESOLUTION. 1.35 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.24
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 3 NUMBER OF REFLECTIONS : 89964
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.162
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 4771
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.35
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39
REMARK 3 REFLECTION IN BIN (WORKING SET) : 6670
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2310
REMARK 3 BIN FREE R VALUE SET COUNT : 356
REMARK 3 BIN FREE R VALUE : 0.2420
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3735
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 4
REMARK 3 SOLVENT ATOMS : 626
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.41
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.62000
REMARK 3 B22 (A**2) : 0.55000
REMARK 3 B33 (A**2) : 0.03000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.26000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.054
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.878
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3765 ; 0.011 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): 3322 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5138 ; 1.950 ; 1.950
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7734 ; 0.946 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 492 ; 6.646 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 586 ; 0.085 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4263 ; 0.009 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 709 ; 0.008 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 758 ; 0.255 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3951 ; 0.250 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): 2101 ; 0.095 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 406 ; 0.154 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.100 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.224 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 44 ; 0.216 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2467 ; 0.736 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3943 ; 1.299 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1298 ; 1.896 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1195 ; 2.982 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : BABINET MODEL WITH MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS. THIS ENTRY CONTAINS ATOMS THAT HAVE BEEN MODELED WITH
REMARK 3 AN OCCUPANCY OF 0.00.
REMARK 4
REMARK 4 1V0W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-04.
REMARK 100 THE DEPOSITION ID IS D_1290014930.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 120.0
REMARK 200 PH : 5.40
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : BM1A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.873
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 89964
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350
REMARK 200 RESOLUTION RANGE LOW (A) : 19.500
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 200 DATA REDUNDANCY : 4.700
REMARK 200 R MERGE (I) : 0.05000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7
REMARK 200 DATA REDUNDANCY IN SHELL : 4.50
REMARK 200 R MERGE FOR SHELL (I) : 0.34400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: BASED ON PDB ENTRY 1F0I
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NH4AC, 0.1 M CITRATE/ PHOSPHATE
REMARK 280 BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER
REMARK 280 BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-
REMARK 280 AMOUNTS OF PHOSPHATE., PH 5.40
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 28.18500
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 400
REMARK 400 COMPOUND
REMARK 400 THIS DATASET DESCRIBES AN 8 HOUR SUBSTRATE SOAK USING 2MM
REMARK 400 DIBUTYRYLPHOSPHATIDYLCHOLINE. A PHOSPHATE IS FOUND TO BE
REMARK 400 COVALENTLY LINKED TO AN ACTIVE SITE HISTIDINE, SUGGESTING
REMARK 400 THAT THE CATALYTIC REACTION CAN PROCEED BEYOND THAT OF
REMARK 400 PRODUCT FORMATION, AND THAT, IN FACT THE PRODUCT CAN
REMARK 400 REENTER THE ACTIVE SITE TO BE FURTHER PROCESSED.THIS
REMARK 400 HISTIDINE IS ALSO FOUND IN A SECOND CONFORMATION WITH
REMARK 400 LOWER OCCUPANCY.
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 ALA A 4
REMARK 465 ASP A 5
REMARK 465 VAL A 127
REMARK 465 TYR A 128
REMARK 465 GLY A 383
REMARK 465 ALA A 384
REMARK 465 VAL A 385
REMARK 465 GLY A 386
REMARK 465 SER A 387
REMARK 465 GLY A 388
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 LYS A 60 CE NZ
REMARK 480 LYS A 68 CG CD CE NZ
REMARK 480 LYS A 115 CE NZ
REMARK 480 VAL A 132 CG1 CG2
REMARK 480 LYS A 136 CG CD CE NZ
REMARK 480 GLU A 140 CG CD OE1 OE2
REMARK 480 LYS A 147 CB CG CD CE NZ
REMARK 480 GLU A 150 CG CD OE1 OE2
REMARK 480 LYS A 163 CD CE NZ
REMARK 480 ASP A 195 CG OD1 OD2
REMARK 480 ILE A 233 CB CG1 CG2 CD1
REMARK 480 ASN A 243 CB CG OD1 ND2
REMARK 480 LYS A 252 CE NZ
REMARK 480 ASP A 279 OD1 OD2
REMARK 480 LYS A 300 CE NZ
REMARK 480 LEU A 306 CD1 CD2
REMARK 480 ARG A 382 CG CD NE CZ NH1 NH2
REMARK 480 LYS A 394 CD CE NZ
REMARK 480 GLN A 415 CG CD OE1 NE2
REMARK 480 LYS A 438 CE NZ
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NZ LYS A 147 O HOH A 2278 2.00
REMARK 500 O HOH A 2129 O HOH A 2130 2.04
REMARK 500 O HOH A 2251 O HOH A 2253 2.13
REMARK 500 NZ LYS A 107 O HOH A 2223 2.14
REMARK 500 NE2 HIS A 129 O HOH A 2253 2.14
REMARK 500 O HOH A 2252 O HOH A 2253 2.17
REMARK 500
REMARK 500 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. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED 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 ND1 HIS A 307 O HOH A 2253 2645 2.14
REMARK 500 O HOH A 2113 O HOH A 2251 2655 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 HIS A 170 CA HIS A 170 CB 0.144
REMARK 500 HIS A 170 NE2 HIS A 170 CD2 -0.082
REMARK 500 LEU A 290 C PRO A 294 N 0.138
REMARK 500 VAL A 302 C VAL A 304 N 0.304
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 HIS A 170 N - CA - CB ANGL. DEV. = 17.6 DEGREES
REMARK 500 ASN A 243 N - CA - CB ANGL. DEV. = -25.7 DEGREES
REMARK 500 LEU A 306 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES
REMARK 500 ARG A 327 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 ASP A 455 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ARG A 83 -51.46 -135.26
REMARK 500 HIS A 170 10.85 -142.23
REMARK 500 ASP A 177 18.59 56.09
REMARK 500 ALA A 234 -29.27 89.17
REMARK 500 SER A 457 -56.02 -138.80
REMARK 500 TRP A 470 52.34 -119.25
REMARK 500 LEU A 491 -59.44 -138.33
REMARK 500 ASN A 513 65.66 -102.20
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 HIS A 170 -11.38
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2038 DISTANCE = 6.34 ANGSTROMS
REMARK 525 HOH A2074 DISTANCE = 6.28 ANGSTROMS
REMARK 525 HOH A2087 DISTANCE = 6.81 ANGSTROMS
REMARK 525 HOH A2127 DISTANCE = 6.53 ANGSTROMS
REMARK 525 HOH A2135 DISTANCE = 7.19 ANGSTROMS
REMARK 525 HOH A2155 DISTANCE = 5.83 ANGSTROMS
REMARK 700
REMARK 700 SHEET
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
REMARK 700 TWO SHEETS ARE DEFINED.
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO3 A1515
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1V0S RELATED DB: PDB
REMARK 900 UNINHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF.
REMARK 900 RELATED ID: 1V0T RELATED DB: PDB
REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE
REMARK 900 PRODUCT GLYCEROPHOSPHATE.
REMARK 900 RELATED ID: 1V0U RELATED DB: PDB
REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE
REMARK 900 PRODUCT GLYCEROPHOSPHATE.
REMARK 900 RELATED ID: 1V0R RELATED DB: PDB
REMARK 900 TUNGSTATE INHIBITED PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN
REMARK 900 RELATED ID: 1V0V RELATED DB: PDB
REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE
REMARK 900 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
REMARK 900 RELATED ID: 1V0Y RELATED DB: PDB
REMARK 900 PHOSPHOLIPASE D FROM STREPTOMYCES SP. STRAIN PMF SOAKED WITH THE
REMARK 900 SUBSTRATE DIBUTYRYLPHOSPHATIDYLCHOLINE.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THIS SEQUENCE HAS NOT BEEN DEPOSITED TO UNIPROT AT THE
REMARK 999 TIME OF STRUCTURE DEPOSITION.
DBREF 1V0W A 4 290 PDB 1V0W 1V0W 4 290
DBREF 1V0W A 294 302 PDB 1V0W 1V0W 294 302
DBREF 1V0W A 304 514 PDB 1V0W 1V0W 304 514
SEQRES 1 A 506 ALA ASP SER ALA THR PRO HIS LEU ASP ALA VAL GLU GLN
SEQRES 2 A 506 THR LEU ARG GLN VAL SER PRO GLY LEU GLU GLY ASP VAL
SEQRES 3 A 506 TRP GLU ARG THR SER GLY ASN LYS LEU ASP GLY SER ALA
SEQRES 4 A 506 ALA ASP PRO SER ASP TRP LEU LEU GLN THR PRO GLY CYS
SEQRES 5 A 506 TRP GLY ASP ASP LYS CYS ALA ASP ARG VAL GLY THR LYS
SEQRES 6 A 506 ARG LEU LEU ALA LYS MET THR GLU ASN ILE GLY ASN ALA
SEQRES 7 A 506 THR ARG THR VAL ASP ILE SER THR LEU ALA PRO PHE PRO
SEQRES 8 A 506 ASN GLY ALA PHE GLN ASP ALA ILE VAL ALA GLY LEU LYS
SEQRES 9 A 506 GLU SER ALA ALA LYS GLY ASN LYS LEU LYS VAL ARG ILE
SEQRES 10 A 506 LEU VAL GLY ALA ALA PRO VAL TYR HIS MET ASN VAL ILE
SEQRES 11 A 506 PRO SER LYS TYR ARG ASP GLU LEU THR ALA LYS LEU GLY
SEQRES 12 A 506 LYS ALA ALA GLU ASN ILE THR LEU ASN VAL ALA SER MET
SEQRES 13 A 506 THR THR SER LYS THR ALA PHE SER TRP ASN HIS SER LYS
SEQRES 14 A 506 ILE LEU VAL VAL ASP GLY GLN SER ALA LEU THR GLY GLY
SEQRES 15 A 506 ILE ASN SER TRP LYS ASP ASP TYR LEU ASP THR THR HIS
SEQRES 16 A 506 PRO VAL SER ASP VAL ASP LEU ALA LEU THR GLY PRO ALA
SEQRES 17 A 506 ALA GLY SER ALA GLY ARG TYR LEU ASP THR LEU TRP THR
SEQRES 18 A 506 TRP THR CYS GLN ASN LYS SER ASN ILE ALA SER VAL TRP
SEQRES 19 A 506 PHE ALA ALA SER GLY ASN ALA GLY CYS MET PRO THR MET
SEQRES 20 A 506 HIS LYS ASP THR ASN PRO LYS ALA SER PRO ALA THR GLY
SEQRES 21 A 506 ASN VAL PRO VAL ILE ALA VAL GLY GLY LEU GLY VAL GLY
SEQRES 22 A 506 ILE LYS ASP VAL ASP PRO LYS SER THR PHE ARG PRO ASP
SEQRES 23 A 506 LEU PRO THR ALA SER ASP THR LYS CYS VAL VAL GLY LEU
SEQRES 24 A 506 HIS ASP ASN THR ASN ALA ASP ARG ASP TYR ASP THR VAL
SEQRES 25 A 506 ASN PRO GLU GLU SER ALA LEU ARG ALA LEU VAL ALA SER
SEQRES 26 A 506 ALA LYS GLY HIS ILE GLU ILE SER GLN GLN ASP LEU ASN
SEQRES 27 A 506 ALA THR CYS PRO PRO LEU PRO ARG TYR ASP ILE ARG LEU
SEQRES 28 A 506 TYR ASP ALA LEU ALA ALA LYS MET ALA ALA GLY VAL LYS
SEQRES 29 A 506 VAL ARG ILE VAL VAL SER ASP PRO ALA ASN ARG GLY ALA
SEQRES 30 A 506 VAL GLY SER GLY GLY TYR SER GLN ILE LYS SER LEU SER
SEQRES 31 A 506 GLU ILE SER ASP THR LEU ARG ASN ARG LEU ALA ASN ILE
SEQRES 32 A 506 THR GLY GLY GLN GLN ALA ALA LYS THR ALA MET CYS SER
SEQRES 33 A 506 ASN LEU GLN LEU ALA THR PHE ARG SER SER PRO ASN GLY
SEQRES 34 A 506 LYS TRP ALA ASP GLY HIS PRO TYR ALA GLN HIS HIS LYS
SEQRES 35 A 506 LEU VAL SER VAL ASP SER SER THR PHE TYR ILE GLY SER
SEQRES 36 A 506 LYS ASN LEU TYR PRO SER TRP LEU GLN ASP PHE GLY TYR
SEQRES 37 A 506 ILE VAL GLU SER PRO GLU ALA ALA LYS GLN LEU ASP ALA
SEQRES 38 A 506 LYS LEU LEU ASP PRO GLN TRP LYS TYR SER GLN GLU THR
SEQRES 39 A 506 ALA THR VAL ASP TYR ALA ARG GLY ILE CYS ASN ALA
HET PO3 A1515 4
HETNAM PO3 PHOSPHITE ION
FORMUL 2 PO3 O3 P 3-
FORMUL 3 HOH *626(H2 O)
HELIX 1 1 THR A 8 SER A 22 1 15
HELIX 2 2 PRO A 23 LEU A 25 5 3
HELIX 3 3 ASP A 44 ASP A 47 5 4
HELIX 4 4 ARG A 64 ASN A 80 1 17
HELIX 5 5 ASN A 95 LYS A 112 1 18
HELIX 6 6 VAL A 132 GLY A 146 1 15
HELIX 7 7 LYS A 147 GLU A 150 5 4
HELIX 8 8 TRP A 189 LEU A 194 1 6
HELIX 9 9 GLY A 209 ASN A 229 1 21
HELIX 10 10 THR A 249 ASN A 255 1 7
HELIX 11 11 ASP A 313 ASN A 320 1 8
HELIX 12 12 ASN A 320 SER A 332 1 13
HELIX 13 13 ASP A 355 ALA A 368 1 14
HELIX 14 14 ASP A 378 ARG A 382 5 5
HELIX 15 15 LEU A 396 GLY A 412 1 17
HELIX 16 16 GLY A 413 ASN A 425 1 12
HELIX 17 17 SER A 480 LEU A 491 1 12
HELIX 18 18 LEU A 491 GLN A 500 1 10
HELIX 19 19 GLU A 501 ALA A 503 5 3
HELIX 20 20 ALA A 508 GLY A 510 5 3
SHEET 1 AA12 LEU A 49 THR A 52 0
SHEET 2 AA12 ASP A 202 THR A 208 -1 O ASP A 202 N THR A 52
SHEET 3 AA12 TRP A 30 LEU A 38 -1 O LYS A 37 N THR A 208
SHEET 4 AA12 VAL A 265 GLY A 271 -1 O VAL A 265 N ASN A 36
SHEET 5 AA12 PHE A 474 GLU A 479 -1 O GLY A 475 N VAL A 270
SHEET 6 AA12 THR A 458 GLY A 462 -1 O PHE A 459 N VAL A 478
SHEET 7 AA12 LYS A 450 VAL A 454 -1 O LYS A 450 N GLY A 462
SHEET 8 AA12 HIS A 336 GLN A 341 -1 O GLU A 338 N SER A 453
SHEET 9 AA12 LYS A 371 VAL A 376 1 O LYS A 371 N ILE A 337
SHEET 10 AA12 LEU A 426 THR A 430 1 O GLN A 427 N ILE A 374
SHEET 11 AA12 VAL A 505 ASP A 506 -1 O VAL A 505 N LEU A 428
SHEET 12 AA12 ILE A 511 CYS A 512 -1 O ILE A 511 N ASP A 506
SHEET 1 AB 8 LEU A 49 THR A 52 0
SHEET 2 AB 8 ASP A 202 THR A 208 -1 O ASP A 202 N THR A 52
SHEET 3 AB 8 SER A 180 GLY A 184 -1 O ALA A 181 N LEU A 207
SHEET 4 AB 8 ILE A 173 VAL A 176 -1 O LEU A 174 N LEU A 182
SHEET 5 AB 8 THR A 84 LEU A 90 -1 O ASP A 86 N VAL A 175
SHEET 6 AB 8 LEU A 116 GLY A 123 1 O LYS A 117 N VAL A 85
SHEET 7 AB 8 ILE A 152 MET A 159 1 O THR A 153 N VAL A 118
SHEET 8 AB 8 VAL A 236 ALA A 240 -1 O TRP A 237 N SER A 158
SSBOND 1 CYS A 55 CYS A 61 1555 1555 2.03
SSBOND 2 CYS A 227 CYS A 246 1555 1555 2.04
SSBOND 3 CYS A 301 CYS A 348 1555 1555 2.02
SSBOND 4 CYS A 423 CYS A 512 1555 1555 2.01
LINK NE2AHIS A 170 P PO3 A1515 1555 1555 1.65
CISPEP 1 THR A 52 PRO A 53 0 -1.25
CISPEP 2 ALA A 91 PRO A 92 0 2.33
CISPEP 3 CYS A 348 PRO A 349 0 -8.15
CISPEP 4 PRO A 349 PRO A 350 0 1.93
SITE 1 AC1 9 HIS A 170 LYS A 172 ASN A 187 HIS A 448
SITE 2 AC1 9 LYS A 450 ASN A 465 HOH A2573 HOH A2625
SITE 3 AC1 9 HOH A2626
CRYST1 57.227 56.370 68.631 90.00 93.69 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 0.017474 0.000000 0.001127 0.00000
SCALE2 0.000000 0.017740 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014601 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
