HEADER HYDROLASE 05-DEC-07 2ZE4 TITLE CRYSTAL STRUCTURE OF PHOSPHOLIPASE D FROM STREPTOMYCES TITLE 2 ANTIBIOTICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHOLINE PHOSPHATASE; COMPND 5 EC: 3.1.4.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES ANTIBIOTICUS; SOURCE 3 ORGANISM_TAXID: 1890; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPELB-PLD3 KEYWDS ALPHA-BETA-BETA-ALPHA-SANDWICH, HYDROLASE, LIPID KEYWDS 2 DEGRADATION, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR A.SUZUKI,K.KAKUNO,R.SAITO,Y.IWASAKI,T.YAMANE,T.YAMANE REVDAT 3 24-FEB-09 2ZE4 1 VERSN REVDAT 2 24-JUN-08 2ZE4 1 REMARK REVDAT 1 25-DEC-07 2ZE4 0 JRNL AUTH A.SUZUKI,K.KAKUNO,R.SAITO,Y.IWASAKI,T.YAMANE, JRNL AUTH 2 T.YAMANE JRNL TITL CRYSTAL STRUCTURE OF PHOSPHOLIPASE D FROM JRNL TITL 2 STREPTOMYCES ANTIBIOTICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.SUZUKI,K.KAKUNO,Y.IWASAKI,T.YAMANE,T.YAMANE REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION REMARK 1 TITL 2 STUDIES OF PHOSPHOLIPASE D FROM STREPTOMYCES REMARK 1 TITL 3 ANTIBIOTICUS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 317 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 10089437 REMARK 1 DOI 10.1107/S0907444998010592 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.MASAYAMA,T.TAKAHASHI,K.TSUKADA,S.NISHIKAWA, REMARK 1 AUTH 2 R.TAKAHASHI,M.ADACHI,K.KOGA,A.SUZUKI,T.YAMANE, REMARK 1 AUTH 3 H.NAKANO,Y.IWASAKI REMARK 1 TITL STREPTOMYCES PHOSPHOLIPASE D MUTANTS WITH ALTERED REMARK 1 TITL 2 SUBSTRATE SPECIFICITY CAPABLE OF REMARK 1 TITL 3 PHOSPHATIDYLINOSITOL SYNTHESIS REMARK 1 REF CHEMBIOCHEM V. 9 974 2008 REMARK 1 REFN ISSN 1439-4227 REMARK 1 PMID 18338352 REMARK 1 DOI 10.1002/CBIC.200700528 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0040 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 15916 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) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 856 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1012 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.1530 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3743 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.16000 REMARK 3 B22 (A**2) : 1.19000 REMARK 3 B33 (A**2) : -1.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 2.239 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.224 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.979 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3844 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5248 ; 1.917 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 500 ; 7.078 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;37.624 ;24.114 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 586 ;17.006 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;24.565 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2953 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1659 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2605 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.125 ; 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): 11 ; 0.168 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.117 ; 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): 2547 ; 1.144 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3995 ; 1.942 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1480 ; 3.159 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1253 ; 5.296 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2ZE4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB027856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17415 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.15100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 50.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 6000, 0.1M MES, PH 6.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 30.50200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.67150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.50400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.67150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.50200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.50400 REMARK 290 SMTRY3 4 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: PISA 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 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 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 ALA A 505 REMARK 465 ARG A 506 REMARK 465 GLN A 507 REMARK 465 ALA A 508 REMARK 465 GLY A 509 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 SER A 282 CB SER A 282 OG -0.079 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 PRO A 5 C - N - CA ANGL. DEV. = -10.3 DEGREES REMARK 500 SER A 282 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 ASP A 373 CB - CG - OD2 ANGL. DEV. = -5.7 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 GLN A 29 131.95 -172.93 REMARK 500 ASP A 42 69.68 -154.35 REMARK 500 SER A 113 70.36 -118.93 REMARK 500 LEU A 164 60.76 60.46 REMARK 500 PRO A 257 128.50 -27.26 REMARK 500 HIS A 286 76.83 -155.66 REMARK 500 ALA A 307 38.29 -142.18 REMARK 500 SER A 330 -49.87 -136.23 REMARK 500 SER A 451 -38.41 -137.86 REMARK 500 SER A 474 114.49 -167.25 REMARK 500 LEU A 485 -54.30 -137.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 254 SER A 255 148.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZE9 RELATED DB: PDB REMARK 900 H168A MUTANT OF PHOSPHOLIPASE D IN COMPLEX WITH REMARK 900 PHOSPHATIDYLCHOLINE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE REMARK 999 DATABASE. ACCORDING TO THE DEPOSITOR, THE SEQUENCE IN REMARK 999 Q53728 CONTAINS SOME ERRORS AND RESIDUE NUMBER 107 IS SER, REMARK 999 211 IS ARG. REMARK 999 THESE ERRORS WILL BE FIXED LATER. DBREF 2ZE4 A 1 509 UNP Q53728 PLD_STRAT 48 556 SEQADV 2ZE4 SER A 107 UNP Q53728 VAL 154 SEE REMARK 999 SEQADV 2ZE4 ARG A 211 UNP Q53728 ALA 258 SEE REMARK 999 SEQRES 1 A 509 ALA ASP THR PRO PRO THR PRO HIS LEU ASP ALA ILE GLU SEQRES 2 A 509 ARG SER LEU ARG ASP THR SER PRO GLY LEU GLU GLY SER SEQRES 3 A 509 VAL TRP GLN ARG THR ASP GLY ASN ARG LEU ASP ALA PRO SEQRES 4 A 509 ASP GLY ASP PRO ALA GLY TRP LEU LEU GLN THR PRO GLY SEQRES 5 A 509 CYS TRP GLY ASP ALA GLY CYS LYS ASP ARG ALA GLY THR SEQRES 6 A 509 ARG ARG LEU LEU ASP LYS MET THR ARG ASN ILE ALA ASP SEQRES 7 A 509 ALA ARG HIS THR VAL ASP ILE SER SER LEU ALA PRO PHE SEQRES 8 A 509 PRO ASN GLY GLY PHE GLU ASP ALA VAL VAL ASP GLY LEU SEQRES 9 A 509 LYS ALA SER VAL ALA ALA GLY HIS SER PRO ARG VAL ARG SEQRES 10 A 509 ILE LEU VAL GLY ALA ALA PRO ILE TYR HIS LEU ASN VAL SEQRES 11 A 509 VAL PRO SER ARG TYR ARG ASP GLU LEU ILE GLY LYS LEU SEQRES 12 A 509 GLY ALA ALA ALA GLY LYS VAL THR LEU ASN VAL ALA SER SEQRES 13 A 509 MET THR THR SER LYS THR SER LEU SER TRP ASN HIS SER SEQRES 14 A 509 LYS LEU LEU VAL VAL ASP GLY LYS THR ALA ILE THR GLY SEQRES 15 A 509 GLY ILE ASN GLY TRP LYS ASP ASP TYR LEU ASP THR ALA SEQRES 16 A 509 HIS PRO VAL SER ASP VAL ASP MET ALA LEU SER GLY PRO SEQRES 17 A 509 ALA ALA ARG SER ALA GLY LYS TYR LEU ASP THR LEU TRP SEQRES 18 A 509 ASP TRP THR CYS ARG ASN ALA SER ASP PRO ALA LYS VAL SEQRES 19 A 509 TRP LEU ALA THR SER ASN GLY ALA SER CYS MET PRO SER SEQRES 20 A 509 MET GLU GLN ASP GLU ALA GLY SER ALA PRO ALA GLU PRO SEQRES 21 A 509 THR GLY ASP VAL PRO VAL ILE ALA VAL GLY GLY LEU GLY SEQRES 22 A 509 VAL GLY ILE LYS GLU SER ASP PRO SER SER GLY TYR HIS SEQRES 23 A 509 PRO ASP LEU PRO THR ALA PRO ASP THR LYS CYS THR VAL SEQRES 24 A 509 GLY LEU HIS ASP ASN THR ASN ALA ASP ARG ASP TYR ASP SEQRES 25 A 509 THR VAL ASN PRO GLU GLU ASN ALA LEU ARG SER LEU ILE SEQRES 26 A 509 ALA SER ALA ARG SER HIS VAL GLU ILE SER GLN GLN ASP SEQRES 27 A 509 LEU ASN ALA THR CYS PRO PRO LEU PRO ARG TYR ASP ILE SEQRES 28 A 509 ARG THR TYR ASP THR LEU ALA GLY LYS LEU ALA ALA GLY SEQRES 29 A 509 VAL LYS VAL ARG ILE VAL VAL SER ASP PRO ALA ASN ARG SEQRES 30 A 509 GLY ALA VAL GLY SER GLY GLY TYR SER GLN ILE LYS SER SEQRES 31 A 509 LEU ASP GLU ILE SER ASP THR LEU ARG THR ARG LEU VAL SEQRES 32 A 509 ALA LEU THR GLY ASP ASN GLU LYS ALA SER ARG ALA LEU SEQRES 33 A 509 CYS GLY ASN LEU GLN LEU ALA SER PHE ARG SER SER ASP SEQRES 34 A 509 ALA ALA LYS TRP ALA ASP GLY LYS PRO TYR ALA LEU HIS SEQRES 35 A 509 HIS LYS LEU VAL SER VAL ASP ASP SER ALA PHE TYR ILE SEQRES 36 A 509 GLY SER LYS ASN LEU TYR PRO ALA TRP LEU GLN ASP PHE SEQRES 37 A 509 GLY TYR ILE VAL GLU SER PRO ALA ALA ALA GLN GLN LEU SEQRES 38 A 509 LYS THR GLU LEU LEU ASP PRO GLU TRP LYS TYR SER GLN SEQRES 39 A 509 GLN ALA ALA ALA THR PRO ALA GLY CYS PRO ALA ARG GLN SEQRES 40 A 509 ALA GLY HET MES A 510 12 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *204(H2 O) HELIX 1 1 THR A 6 SER A 20 1 15 HELIX 2 2 PRO A 21 GLU A 24 5 4 HELIX 3 3 ARG A 62 ASP A 78 1 17 HELIX 4 4 ASN A 93 ALA A 110 1 18 HELIX 5 5 VAL A 131 GLY A 144 1 14 HELIX 6 6 ALA A 145 VAL A 150 5 6 HELIX 7 7 TRP A 187 LEU A 192 1 6 HELIX 8 8 GLY A 207 ALA A 228 1 22 HELIX 9 9 SER A 247 GLY A 254 1 8 HELIX 10 10 ASP A 308 ASN A 315 1 8 HELIX 11 11 ASN A 315 SER A 327 1 13 HELIX 12 12 ASP A 350 ALA A 363 1 14 HELIX 13 13 ASP A 373 ARG A 377 5 5 HELIX 14 14 LEU A 391 GLY A 407 1 17 HELIX 15 15 ASP A 408 ASN A 419 1 12 HELIX 16 16 SER A 474 LEU A 485 1 12 HELIX 17 17 LEU A 485 GLN A 494 1 10 HELIX 18 18 GLN A 495 ALA A 497 5 3 SHEET 1 A 8 LEU A 47 THR A 50 0 SHEET 2 A 8 ASP A 200 SER A 206 -1 O ASP A 200 N THR A 50 SHEET 3 A 8 THR A 178 GLY A 182 -1 N ALA A 179 O LEU A 205 SHEET 4 A 8 LEU A 171 VAL A 174 -1 N VAL A 174 O THR A 178 SHEET 5 A 8 THR A 82 LEU A 88 -1 N ASP A 84 O VAL A 173 SHEET 6 A 8 ARG A 115 GLY A 121 1 O ARG A 117 N ILE A 85 SHEET 7 A 8 THR A 151 SER A 160 1 O THR A 151 N VAL A 116 SHEET 8 A 8 VAL A 234 THR A 238 -1 O ALA A 237 N VAL A 154 SHEET 1 B15 SER A 165 TRP A 166 0 SHEET 2 B15 THR A 151 SER A 160 -1 N SER A 160 O SER A 165 SHEET 3 B15 ARG A 115 GLY A 121 1 N VAL A 116 O THR A 151 SHEET 4 B15 THR A 82 LEU A 88 1 N ILE A 85 O ARG A 117 SHEET 5 B15 LEU A 171 VAL A 174 -1 O VAL A 173 N ASP A 84 SHEET 6 B15 THR A 178 GLY A 182 -1 O THR A 178 N VAL A 174 SHEET 7 B15 ASP A 200 SER A 206 -1 O LEU A 205 N ALA A 179 SHEET 8 B15 TRP A 28 LEU A 36 -1 N ARG A 35 O SER A 206 SHEET 9 B15 VAL A 264 LEU A 272 -1 O ALA A 268 N GLN A 29 SHEET 10 B15 GLN A 466 GLU A 473 -1 O ILE A 471 N ILE A 267 SHEET 11 B15 ALA A 452 GLY A 456 -1 N ILE A 455 O TYR A 470 SHEET 12 B15 LYS A 444 VAL A 448 -1 N VAL A 448 O ALA A 452 SHEET 13 B15 HIS A 331 GLN A 336 -1 N GLU A 333 O SER A 447 SHEET 14 B15 LYS A 366 VAL A 371 1 O ARG A 368 N ILE A 334 SHEET 15 B15 LEU A 420 SER A 424 1 O GLN A 421 N ILE A 369 SSBOND 1 CYS A 53 CYS A 59 1555 1555 2.01 SSBOND 2 CYS A 225 CYS A 244 1555 1555 2.03 SSBOND 3 CYS A 297 CYS A 343 1555 1555 2.03 SSBOND 4 CYS A 417 CYS A 503 1555 1555 2.01 CISPEP 1 THR A 50 PRO A 51 0 0.18 CISPEP 2 ALA A 89 PRO A 90 0 3.27 CISPEP 3 CYS A 343 PRO A 344 0 -11.10 CISPEP 4 PRO A 344 PRO A 345 0 3.04 SITE 1 AC1 4 SER A 156 ALA A 232 LYS A 233 HOH A 596 CRYST1 61.004 85.008 99.343 90.00 90.00 90.00 P 21 21 21 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 0.016392 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010066 0.00000