HEADER HYDROLASE 26-APR-22 7ZOM TITLE CRYSTAL STRUCTURE OF N-TERMINAL CATALYTIC DOMAIN OF HUMAN PLAAT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A AND ACYLTRANSFERASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADIPOSE-SPECIFIC PHOSPHOLIPASE A2,ADPLA,GROUP XVI COMPND 5 PHOSPHOLIPASE A1/A2,H-REV 107 PROTEIN HOMOLOG,H-REV107,HREV107-1, COMPND 6 HRAS-LIKE SUPPRESSOR 1,HRAS-LIKE SUPPRESSOR 3,HRSL3,HREV107-3,RENAL COMPND 7 CARCINOMA ANTIGEN NY-REN-65; COMPND 8 EC: 2.3.1.-,3.1.1.32,3.1.1.4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLAAT3, HRASLS3, HREV107, PLA2G16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NLPC/P60, CATALYTIC DOMAIN, PHOSPHOLIPASE A AND ACYLTRANSFERASE, KEYWDS 2 ENTEROVIRUS HOST FACTOR, MEMBRANE REMODELLING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.VON CASTELMUR,A.PERRAKIS REVDAT 2 19-JUN-24 7ZOM 1 REMARK REVDAT 1 26-APR-23 7ZOM 0 JRNL AUTH E.VON CASTELMUR,A.PERRAKIS JRNL TITL CRYSTAL STRUCTURE OF N-TERMINAL CATALYTIC DOMAIN OF HUMAN JRNL TITL 2 PLAAT3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21184 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1420 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 853 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05600 REMARK 3 B22 (A**2) : 1.05600 REMARK 3 B33 (A**2) : -3.42600 REMARK 3 B12 (A**2) : 0.52800 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): 0.074 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 968 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1326 ; 1.313 ; 1.657 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 121 ; 5.675 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 53 ;25.111 ;22.453 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 175 ;11.659 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;16.212 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 122 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 733 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 353 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 635 ; 0.313 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 51 ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 438 ; 5.464 ; 3.309 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 549 ; 6.221 ; 4.904 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 530 ;11.047 ; 4.042 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 767 ;11.664 ; 5.765 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 PLUS 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 USED IF PRESENT IN REMARK 3 THE INPUT FILE REMARK 4 REMARK 4 7ZOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-22. REMARK 100 THE DEPOSITION ID IS D_1292122600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97632 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.03300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.65100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH PH7.0-7.5, 45-70% MPD, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.68967 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.37933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 49.37933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.68967 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 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 MET A 1 REMARK 465 ARG A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 GLU A 41 REMARK 465 VAL A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 ALA A 45 REMARK 465 GLY A 46 REMARK 465 ALA A 47 REMARK 465 ALA A 48 REMARK 465 SER A 49 REMARK 465 VAL A 50 REMARK 465 MET A 51 REMARK 465 SER A 52 REMARK 465 ALA A 53 REMARK 465 LEU A 54 REMARK 465 THR A 55 REMARK 465 ASP A 56 REMARK 465 ARG A 126 REMARK 465 SER A 127 REMARK 465 ASP A 128 REMARK 465 GLN A 129 REMARK 465 VAL A 130 REMARK 465 ARG A 131 REMARK 465 ASP A 132 DBREF 7ZOM A 1 132 UNP P53816 PLAT3_HUMAN 1 132 SEQRES 1 A 132 MET ARG ALA PRO ILE PRO GLU PRO LYS PRO GLY ASP LEU SEQRES 2 A 132 ILE GLU ILE PHE ARG PRO PHE TYR ARG HIS TRP ALA ILE SEQRES 3 A 132 TYR VAL GLY ASP GLY TYR VAL VAL HIS LEU ALA PRO PRO SEQRES 4 A 132 SER GLU VAL ALA GLY ALA GLY ALA ALA SER VAL MET SER SEQRES 5 A 132 ALA LEU THR ASP LYS ALA ILE VAL LYS LYS GLU LEU LEU SEQRES 6 A 132 TYR ASP VAL ALA GLY SER ASP LYS TYR GLN VAL ASN ASN SEQRES 7 A 132 LYS HIS ASP ASP LYS TYR SER PRO LEU PRO CYS SER LYS SEQRES 8 A 132 ILE ILE GLN ARG ALA GLU GLU LEU VAL GLY GLN GLU VAL SEQRES 9 A 132 LEU TYR LYS LEU THR SER GLU ASN CYS GLU HIS PHE VAL SEQRES 10 A 132 ASN GLU LEU ARG TYR GLY VAL ALA ARG SER ASP GLN VAL SEQRES 11 A 132 ARG ASP HET MPD A 201 8 HET MPD A 202 8 HET MPD A 203 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 2 MPD 3(C6 H14 O2) FORMUL 5 HOH *51(H2 O) HELIX 1 AA1 LEU A 65 GLY A 70 1 6 HELIX 2 AA2 PRO A 88 LEU A 99 1 12 HELIX 3 AA3 THR A 109 GLY A 123 1 15 SHEET 1 AA1 6 LYS A 73 VAL A 76 0 SHEET 2 AA1 6 LEU A 13 ARG A 18 -1 N GLU A 15 O GLN A 75 SHEET 3 AA1 6 TYR A 21 GLY A 29 -1 O HIS A 23 N ILE A 16 SHEET 4 AA1 6 TYR A 32 ALA A 37 -1 O TYR A 32 N VAL A 28 SHEET 5 AA1 6 ALA A 58 LEU A 64 -1 O ILE A 59 N ALA A 37 SHEET 6 AA1 6 GLU A 103 VAL A 104 -1 O VAL A 104 N ALA A 58 CRYST1 60.638 60.638 74.069 90.00 90.00 120.00 P 31 2 1 6 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 0.016491 0.009521 0.000000 0.00000 SCALE2 0.000000 0.019043 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013501 0.00000