HEADER HYDROLASE 06-AUG-15 5D3K TITLE CRYSTAL STRUCTURE OF THE THIOESTERASE DOMAIN OF DEOXYERYTHRONOLIDE B TITLE 2 SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERYTHRONOLIDE SYNTHASE, MODULES 5 AND 6; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2904-3172; COMPND 5 SYNONYM: 6-DEOXYERYTHRONOLIDE B SYNTHASE III,DEBS 3,ORF 3; COMPND 6 EC: 2.3.1.94; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROPOLYSPORA ERYTHRAEA; SOURCE 3 ORGANISM_TAXID: 1836; SOURCE 4 GENE: ERYA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBACP KEYWDS THIOESTERASE DOMAINE ALPHA / BETA HYDROLASE FOLD DEOXYERYTHRONOLIDE B KEYWDS 2 SYNTHASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.BERGERET,P.ARGYROPOULOS,C.N.BODDY,T.M.SCHMEING REVDAT 3 08-JAN-20 5D3K 1 JRNL REMARK REVDAT 2 13-JAN-16 5D3K 1 JRNL REVDAT 1 09-DEC-15 5D3K 0 JRNL AUTH P.ARGYROPOULOS,F.BERGERET,C.PARDIN,J.M.REIMER,A.PINTO, JRNL AUTH 2 C.N.BODDY,T.M.SCHMEING JRNL TITL TOWARDS A CHARACTERIZATION OF THE STRUCTURAL DETERMINANTS OF JRNL TITL 2 SPECIFICITY IN THE MACROCYCLIZING THIOESTERASE FOR JRNL TITL 3 DEOXYERYTHRONOLIDE B BIOSYNTHESIS. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1860 486 2015 JRNL REFN ISSN 0006-3002 JRNL PMID 26592346 JRNL DOI 10.1016/J.BBAGEN.2015.11.007 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 32914 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1638 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2436 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.01000 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): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.758 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2101 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1929 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2865 ; 1.995 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4437 ; 0.964 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.395 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;26.522 ;22.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 285 ;12.589 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 310 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2422 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 478 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1084 ; 1.765 ; 1.413 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1084 ; 1.759 ; 1.412 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1357 ; 2.577 ; 2.109 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5D3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212609. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 36.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : 0.06900 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC 5.8.0073 REMARK 200 STARTING MODEL: 1KEZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-CACODYLATE, 35-38% REMARK 280 POLYETHYLENE GLYCOL , 0.18-0.24 M CA-ACETATE, PEG300, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+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 -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 0.00000 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 0.00000 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 0.00000 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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 67 CG CD OE1 OE2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 LYS A 134 CG CD CE NZ REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 243 CE NZ REMARK 470 SER A 283 O 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 O HOH A 612 O HOH A 613 1.69 REMARK 500 O HOH A 612 O HOH A 615 1.87 REMARK 500 O HOH A 437 O HOH A 570 1.89 REMARK 500 O HOH A 482 O HOH A 603 1.99 REMARK 500 O HOH A 401 O HOH A 529 2.03 REMARK 500 O HOH A 600 O HOH A 609 2.07 REMARK 500 O HOH A 408 O HOH A 425 2.12 REMARK 500 O HOH A 408 O HOH A 491 2.18 REMARK 500 O HOH A 489 O HOH A 497 2.18 REMARK 500 O HOH A 402 O HOH A 536 2.18 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 GLU A 184 CD GLU A 184 OE1 0.082 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 ASP A 49 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 129 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 199 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 202 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 211 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 211 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 219 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 219 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 258 CB - CG - OD1 ANGL. DEV. = 6.7 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 SER A 142 -129.40 59.61 REMARK 500 GLN A 264 -85.10 -123.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1PE A 302 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 HOH A 411 O 105.8 REMARK 620 3 HOH A 568 O 83.0 92.2 REMARK 620 4 VAL A 27 O 41.0 141.3 99.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 108 OE2 REMARK 620 2 ASP A 199 OD2 108.1 REMARK 620 3 HOH A 500 O 78.4 172.9 REMARK 620 4 GLY A 279 O 84.4 39.5 141.2 REMARK 620 5 GLY A 281 O 86.6 36.1 144.6 3.5 REMARK 620 6 HOH A 540 O 84.8 86.5 97.1 115.9 113.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 275 OD1 REMARK 620 2 HOH A 469 O 78.9 REMARK 620 3 HOH A 446 O 68.6 147.0 REMARK 620 4 HOH A 459 O 99.7 89.8 90.0 REMARK 620 5 GLU A 107 OE1 56.2 74.2 82.9 44.5 REMARK 620 6 GLU A 107 OE2 53.9 74.3 81.8 46.6 2.3 REMARK 620 7 HOH A 575 O 93.4 94.6 92.9 166.8 148.7 146.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D2R RELATED DB: PDB DBREF 5D3K A 15 283 UNP Q03133 ERYA3_SACER 2904 3172 SEQRES 1 A 269 SER SER ALA LEU ARG ASP GLY TYR ARG GLN ALA GLY VAL SEQRES 2 A 269 SER GLY ARG VAL ARG SER TYR LEU ASP LEU LEU ALA GLY SEQRES 3 A 269 LEU SER ASP PHE ARG GLU HIS PHE ASP GLY SER ASP GLY SEQRES 4 A 269 PHE SER LEU ASP LEU VAL ASP MET ALA ASP GLY PRO GLY SEQRES 5 A 269 GLU VAL THR VAL ILE CYS CYS ALA GLY THR ALA ALA ILE SEQRES 6 A 269 SER GLY PRO HIS GLU PHE THR ARG LEU ALA GLY ALA LEU SEQRES 7 A 269 ARG GLY ILE ALA PRO VAL ARG ALA VAL PRO GLN PRO GLY SEQRES 8 A 269 TYR GLU GLU GLY GLU PRO LEU PRO SER SER MET ALA ALA SEQRES 9 A 269 VAL ALA ALA VAL GLN ALA ASP ALA VAL ILE ARG THR GLN SEQRES 10 A 269 GLY ASP LYS PRO PHE VAL VAL ALA GLY HIS SER ALA GLY SEQRES 11 A 269 ALA LEU MET ALA TYR ALA LEU ALA THR GLU LEU LEU ASP SEQRES 12 A 269 ARG GLY HIS PRO PRO ARG GLY VAL VAL LEU ILE ASP VAL SEQRES 13 A 269 TYR PRO PRO GLY HIS GLN ASP ALA MET ASN ALA TRP LEU SEQRES 14 A 269 GLU GLU LEU THR ALA THR LEU PHE ASP ARG GLU THR VAL SEQRES 15 A 269 ARG MET ASP ASP THR ARG LEU THR ALA LEU GLY ALA TYR SEQRES 16 A 269 ASP ARG LEU THR GLY GLN TRP ARG PRO ARG GLU THR GLY SEQRES 17 A 269 LEU PRO THR LEU LEU VAL SER ALA GLY GLU PRO MET GLY SEQRES 18 A 269 PRO TRP PRO ASP ASP SER TRP LYS PRO THR TRP PRO PHE SEQRES 19 A 269 GLU HIS ASP THR VAL ALA VAL PRO GLY ASP HIS PHE THR SEQRES 20 A 269 MET VAL GLN GLU HIS ALA ASP ALA ILE ALA ARG HIS ILE SEQRES 21 A 269 ASP ALA TRP LEU GLY GLY GLY ASN SER HET 1PE A 301 16 HET 1PE A 302 13 HET CA A 303 1 HET CA A 304 1 HET CA A 305 1 HETNAM 1PE PENTAETHYLENE GLYCOL HETNAM CA CALCIUM ION HETSYN 1PE PEG400 FORMUL 2 1PE 2(C10 H22 O6) FORMUL 4 CA 3(CA 2+) FORMUL 7 HOH *224(H2 O) HELIX 1 AA1 SER A 16 SER A 28 1 13 HELIX 2 AA2 ARG A 30 ASP A 43 1 14 HELIX 3 AA3 GLY A 81 GLU A 84 5 4 HELIX 4 AA4 PHE A 85 ARG A 93 1 9 HELIX 5 AA5 SER A 115 GLY A 132 1 18 HELIX 6 AA6 SER A 142 ARG A 158 1 17 HELIX 7 AA7 GLN A 176 TRP A 182 1 7 HELIX 8 AA8 TRP A 182 ARG A 193 1 12 HELIX 9 AA9 ASP A 199 TRP A 216 1 18 HELIX 10 AB1 PHE A 260 GLN A 264 5 5 HELIX 11 AB2 HIS A 266 GLY A 279 1 14 SHEET 1 AA1 2 HIS A 47 PHE A 48 0 SHEET 2 AA1 2 LEU A 112 PRO A 113 1 O LEU A 112 N PHE A 48 SHEET 1 AA2 7 VAL A 59 ALA A 62 0 SHEET 2 AA2 7 VAL A 98 VAL A 101 -1 O ALA A 100 N VAL A 59 SHEET 3 AA2 7 THR A 69 CYS A 73 1 N CYS A 72 O ARG A 99 SHEET 4 AA2 7 PHE A 136 HIS A 141 1 O ALA A 139 N CYS A 73 SHEET 5 AA2 7 GLY A 164 ILE A 168 1 O ILE A 168 N GLY A 140 SHEET 6 AA2 7 THR A 225 ALA A 230 1 O LEU A 226 N LEU A 167 SHEET 7 AA2 7 ASP A 251 VAL A 255 1 O ASP A 251 N LEU A 227 LINK OD2 ASP A 49 CA CA A 303 1555 1555 2.27 LINK OE2 GLU A 108 CA CA A 304 1555 1555 2.08 LINK OD2 ASP A 199 CA CA A 304 1555 1555 2.34 LINK OD1 ASP A 275 CA CA A 305 1555 1555 2.36 LINK CA CA A 303 O HOH A 411 1555 1555 2.44 LINK CA CA A 303 O HOH A 568 1555 1555 2.34 LINK CA CA A 304 O HOH A 500 1555 1555 2.37 LINK CA CA A 305 O HOH A 469 1555 1555 2.34 LINK CA CA A 305 O HOH A 446 1555 1555 2.45 LINK CA CA A 305 O HOH A 459 1555 1555 2.33 LINK O VAL A 27 CA CA A 303 1555 1554 2.28 LINK OE1 GLU A 107 CA CA A 305 1555 2865 2.44 LINK OE2 GLU A 107 CA CA A 305 1555 2865 2.49 LINK O GLY A 279 CA CA A 304 1555 3785 2.36 LINK O GLY A 281 CA CA A 304 1555 3785 2.23 LINK CA CA A 304 O HOH A 540 1555 2865 2.47 LINK CA CA A 305 O HOH A 575 1555 3785 2.44 SITE 1 AC1 8 HIS A 83 ARG A 87 HIS A 141 THR A 195 SITE 2 AC1 8 HOH A 406 HOH A 536 HOH A 550 HOH A 566 SITE 1 AC2 9 TYR A 22 VAL A 31 GLN A 176 MET A 179 SITE 2 AC2 9 LEU A 183 THR A 187 ASP A 210 THR A 213 SITE 3 AC2 9 GLY A 214 SITE 1 AC3 4 VAL A 27 ASP A 49 HOH A 411 HOH A 568 SITE 1 AC4 3 GLU A 108 ASP A 199 HOH A 500 SITE 1 AC5 4 ASP A 275 HOH A 446 HOH A 459 HOH A 469 CRYST1 112.920 112.920 42.970 90.00 90.00 120.00 P 3 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 0.008856 0.005113 0.000000 0.00000 SCALE2 0.000000 0.010226 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023272 0.00000 MASTER 410 0 5 11 9 0 8 6 0 0 0 21 END