HEADER HYDROLASE 23-FEB-18 5ZDM TITLE THE LIGAND-FREE STRUCTURE OF FOMD COMPND MOL_ID: 1; COMPND 2 MOLECULE: FOMD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES FRADIAE; SOURCE 3 ORGANISM_COMMON: STREPTOMYCES ROSEOFLAVUS; SOURCE 4 ORGANISM_TAXID: 1906; SOURCE 5 GENE: FOMD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIS8 KEYWDS METALLOPROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SATO,A.MIYANAGA,F.KUDO,T.EGUCHI REVDAT 3 22-NOV-23 5ZDM 1 LINK REVDAT 2 29-AUG-18 5ZDM 1 JRNL REVDAT 1 25-JUL-18 5ZDM 0 JRNL AUTH S.SATO,A.MIYANAGA,S.Y.KIM,T.KUZUYAMA,F.KUDO,T.EGUCHI JRNL TITL BIOCHEMICAL AND STRUCTURAL ANALYSIS OF FOMD THAT CATALYZES JRNL TITL 2 THE HYDROLYSIS OF CYTIDYLYL ( S)-2-HYDROXYPROPYLPHOSPHONATE JRNL TITL 3 IN FOSFOMYCIN BIOSYNTHESIS. JRNL REF BIOCHEMISTRY V. 57 4858 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 30010320 JRNL DOI 10.1021/ACS.BIOCHEM.8B00690 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 34427 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1756 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2512 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1619 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.81000 REMARK 3 B22 (A**2) : -1.38000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.42000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.970 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1724 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1535 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2354 ; 2.384 ; 1.904 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3512 ; 1.028 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 203 ; 6.589 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;35.751 ;22.105 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 244 ;13.469 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;18.276 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 233 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1986 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 461 ; 0.002 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 207 REMARK 3 RESIDUE RANGE : A 301 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 8.8480 -0.5990 9.2160 REMARK 3 T TENSOR REMARK 3 T11: 0.0527 T22: 0.1219 REMARK 3 T33: 0.0038 T12: 0.0041 REMARK 3 T13: 0.0058 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 0.3163 L22: 0.5846 REMARK 3 L33: 0.6243 L12: -0.2193 REMARK 3 L13: -0.1859 L23: 0.0466 REMARK 3 S TENSOR REMARK 3 S11: 0.0257 S12: 0.0136 S13: -0.0065 REMARK 3 S21: -0.0428 S22: -0.0578 S23: 0.0256 REMARK 3 S31: 0.0349 S32: -0.0459 S33: 0.0321 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 REMARK 4 REMARK 4 5ZDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36195 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3EXM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, CALCIUM CHLORIDE, PEG 8000, REMARK 280 TRIMETHYLAMINE N-OXIDE, CYTOSINE, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 278K 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 23.10750 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 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 ALA A 4 REMARK 465 ALA A 5 REMARK 465 SER A 6 REMARK 465 GLU A 7 REMARK 465 GLY A 8 REMARK 465 THR A 9 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 OD1 ASP A 170 NH2 ARG A 173 1.99 REMARK 500 O HOH A 574 O HOH A 602 2.18 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 O HOH A 509 O HOH A 552 2655 2.15 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 ARG A 20 CZ ARG A 20 NH1 -0.115 REMARK 500 GLU A 145 CG GLU A 145 CD 0.116 REMARK 500 GLU A 145 CD GLU A 145 OE1 0.082 REMARK 500 GLU A 148 CD GLU A 148 OE1 -0.073 REMARK 500 GLU A 159 CG GLU A 159 CD 0.095 REMARK 500 TRP A 182 CE3 TRP A 182 CZ3 0.103 REMARK 500 SER A 207 CA SER A 207 CB -0.128 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 35 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 53 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 137 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 152 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 GLU A 159 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ASP A 183 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 SER A 207 N - CA - CB ANGL. DEV. = 12.0 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 GLU A 127 -54.72 67.87 REMARK 500 ASN A 196 -158.08 -103.96 REMARK 500 THR A 204 76.97 -113.17 REMARK 500 REMARK 500 REMARK: NULL 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 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 109 OD1 REMARK 620 2 ASP A 125 OD1 91.4 REMARK 620 3 ASP A 129 OD1 99.8 150.3 REMARK 620 4 GLU A 205 OE1 88.7 42.8 162.7 REMARK 620 5 GLU A 205 OE2 85.9 41.2 165.6 3.3 REMARK 620 6 HOH A 442 O 170.6 83.7 88.3 82.3 85.1 REMARK 620 7 HOH A 459 O 90.6 76.4 76.1 119.1 117.3 96.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 127 O REMARK 620 2 GLU A 127 OE1 82.4 REMARK 620 3 ASP A 129 OD1 74.1 150.0 REMARK 620 4 ASP A 129 OD2 84.9 148.6 47.9 REMARK 620 5 ASP A 143 OD2 119.6 82.7 125.1 78.9 REMARK 620 6 HOH A 433 O 159.6 109.3 88.9 92.0 79.3 REMARK 620 7 HOH A 442 O 89.6 84.9 76.7 123.7 146.1 75.4 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 CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 305 DBREF 5ZDM A 1 207 UNP D2SNF7 D2SNF7_STRFR 1 207 SEQADV 5ZDM GLY A -3 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDM SER A -2 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDM HIS A -1 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDM GLY A 0 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDM PHE A 139 UNP D2SNF7 LEU 139 ENGINEERED MUTATION SEQRES 1 A 211 GLY SER HIS GLY MET THR GLU ALA ALA SER GLU GLY THR SEQRES 2 A 211 GLU SER PHE ALA PHE GLY ALA VAL VAL GLU ARG ARG ASP SEQRES 3 A 211 GLU LEU ASP GLY ARG PRO TRP ILE SER TYR PRO VAL ARG SEQRES 4 A 211 VAL VAL ALA ASP THR PRO GLU LEU VAL ALA VAL HIS LEU SEQRES 5 A 211 SER HIS GLY THR ARG LEU THR PHE GLY ASP ASP PRO PHE SEQRES 6 A 211 SER TRP GLY PRO HIS PRO TRP GLN LEU PHE GLY ASP ARG SEQRES 7 A 211 TRP GLN SER ALA GLY ILE LEU GLN LEU HIS ARG PRO GLY SEQRES 8 A 211 ARG GLY HIS SER VAL TRP VAL LEU ARG ASP ALA ASP THR SEQRES 9 A 211 GLY ALA PHE ARG GLU TRP TYR VAL ASN VAL GLU ALA PRO SEQRES 10 A 211 TRP ARG ARG THR PRO THR GLY PHE SER THR LEU ASP HIS SEQRES 11 A 211 GLU ILE ASP LEU VAL VAL PRO ALA ASP SER ARG THR PHE SEQRES 12 A 211 ARG TRP LYS ASP VAL GLU LYS PHE GLU GLU ARG ALA ARG SEQRES 13 A 211 ILE GLY HIS PHE SER PRO GLU GLU ALA THR ALA ILE ARG SEQRES 14 A 211 ALA GLU ALA ALA ASP VAL ALA ARG GLU ILE ALA ALA GLY SEQRES 15 A 211 GLU GLN TRP TRP ASP THR ARG TRP SER ARG TRP GLU PRO SEQRES 16 A 211 PRO ALA GLY TRP ASN ALA LEU LEU GLN SER PHE GLU THR SEQRES 17 A 211 GLU GLY SER HET CA A 301 1 HET CA A 302 1 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 6 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CA 2(CA 2+) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 HOH *210(H2 O) HELIX 1 AA1 HIS A 66 GLY A 72 5 7 HELIX 2 AA2 ASP A 143 ILE A 153 1 11 HELIX 3 AA3 SER A 157 ALA A 177 1 21 HELIX 4 AA4 ASP A 183 TRP A 189 5 7 SHEET 1 AA1 5 THR A 55 PHE A 56 0 SHEET 2 AA1 5 ARG A 27 THR A 40 -1 N SER A 31 O THR A 55 SHEET 3 AA1 5 VAL A 17 LEU A 24 -1 N ASP A 22 O TRP A 29 SHEET 4 AA1 5 GLY A 120 THR A 123 1 O THR A 123 N GLU A 23 SHEET 5 AA1 5 ARG A 115 THR A 117 -1 N THR A 117 O GLY A 120 SHEET 1 AA2 8 THR A 55 PHE A 56 0 SHEET 2 AA2 8 ARG A 27 THR A 40 -1 N SER A 31 O THR A 55 SHEET 3 AA2 8 LEU A 43 LEU A 48 -1 O ALA A 45 N VAL A 37 SHEET 4 AA2 8 ILE A 80 HIS A 84 -1 O HIS A 84 N VAL A 44 SHEET 5 AA2 8 HIS A 90 ARG A 96 -1 O VAL A 92 N LEU A 83 SHEET 6 AA2 8 PHE A 103 GLU A 111 -1 O ARG A 104 N LEU A 95 SHEET 7 AA2 8 ASP A 125 PRO A 133 -1 O LEU A 130 N VAL A 108 SHEET 8 AA2 8 ARG A 140 LYS A 142 -1 O LYS A 142 N ASP A 129 LINK OD1 ASN A 109 CA CA A 301 1555 1555 2.21 LINK OD1 ASP A 125 CA CA A 301 1555 1555 2.39 LINK O GLU A 127 CA CA A 302 1555 1555 2.29 LINK OE1 GLU A 127 CA CA A 302 1555 1555 2.32 LINK OD1 ASP A 129 CA CA A 301 1555 1555 2.38 LINK OD1 ASP A 129 CA CA A 302 1555 1555 2.85 LINK OD2 ASP A 129 CA CA A 302 1555 1555 2.37 LINK OD2 ASP A 143 CA CA A 302 1555 1555 2.37 LINK OE1 GLU A 205 CA CA A 301 1555 2555 2.46 LINK OE2 GLU A 205 CA CA A 301 1555 2555 2.45 LINK CA CA A 301 O HOH A 442 1555 1555 2.43 LINK CA CA A 301 O HOH A 459 1555 1555 2.40 LINK CA CA A 302 O HOH A 433 1555 2545 2.30 LINK CA CA A 302 O HOH A 442 1555 1555 2.53 CISPEP 1 ASP A 59 PRO A 60 0 1.46 SITE 1 AC1 5 ASN A 109 ASP A 125 ASP A 129 HOH A 442 SITE 2 AC1 5 HOH A 459 SITE 1 AC2 4 GLU A 127 ASP A 129 ASP A 143 HOH A 442 SITE 1 AC3 9 ARG A 20 ASP A 22 ILE A 30 TYR A 32 SITE 2 AC3 9 HIS A 66 TRP A 68 TRP A 93 ASP A 125 SITE 3 AC3 9 HOH A 410 SITE 1 AC4 6 SER A 136 ARG A 137 PHE A 139 ILE A 175 SITE 2 AC4 6 HOH A 414 HOH A 458 SITE 1 AC5 4 GLU A 105 ARG A 140 HOH A 413 HOH A 416 CRYST1 40.474 46.215 52.504 90.00 110.27 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 0.024707 0.000000 0.009126 0.00000 SCALE2 0.000000 0.021638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020304 0.00000