HEADER HYDROLASE 23-FEB-18 5ZDN TITLE THE COMPLEX STRUCTURE OF FOMD WITH CDP 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 5ZDN 1 LINK REVDAT 2 29-AUG-18 5ZDN 1 JRNL REVDAT 1 25-JUL-18 5ZDN 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. 2.02 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13449 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 693 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 967 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.4330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1575 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.62000 REMARK 3 B22 (A**2) : -1.00000 REMARK 3 B33 (A**2) : -0.62000 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): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1674 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1481 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2293 ; 2.044 ; 1.917 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3384 ; 0.937 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 193 ; 6.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;38.214 ;21.889 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 231 ;14.633 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.124 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 227 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1904 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 451 ; 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): 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 11 A 202 REMARK 3 RESIDUE RANGE : A 301 A 306 REMARK 3 ORIGIN FOR THE GROUP (A): 17.1830 13.6670 33.7400 REMARK 3 T TENSOR REMARK 3 T11: 0.0402 T22: 0.1661 REMARK 3 T33: 0.1543 T12: -0.0007 REMARK 3 T13: 0.0130 T23: 0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.3314 L22: 1.0957 REMARK 3 L33: 0.9664 L12: -0.0924 REMARK 3 L13: -0.0044 L23: -0.2459 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: 0.0598 S13: -0.0599 REMARK 3 S21: 0.1957 S22: -0.0195 S23: 0.0896 REMARK 3 S31: -0.1130 S32: -0.0234 S33: 0.0379 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 5ZDN 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_1300006889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-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 : 14166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 43.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, MAGNESIUM CHLORIDE, PEG REMARK 280 8000, ETOH, CDP, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.28300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.28300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 28.08250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.72600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.08250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.72600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.28300 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.08250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.72600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.28300 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.08250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.72600 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 56.16500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.28300 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 305 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 426 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 441 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 463 LIES ON A SPECIAL POSITION. 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 465 GLU A 10 REMARK 465 GLU A 203 REMARK 465 THR A 204 REMARK 465 GLU A 205 REMARK 465 GLY A 206 REMARK 465 SER A 207 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 438 O HOH A 450 1.84 REMARK 500 O HOH A 421 O HOH A 450 2.02 REMARK 500 O HOH A 421 O HOH A 438 2.11 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 ASP A 39 84.29 -151.91 REMARK 500 GLU A 127 -37.59 57.62 REMARK 500 ASN A 196 -158.46 -109.25 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 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 109 OD1 REMARK 620 2 ASP A 125 OD2 92.6 REMARK 620 3 ASP A 129 OD1 91.0 166.9 REMARK 620 4 HOH A 402 O 102.2 81.5 85.5 REMARK 620 5 HOH A 438 O 141.2 98.1 86.8 116.1 REMARK 620 6 HOH A 450 O 91.4 103.1 89.4 165.5 49.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 127 O REMARK 620 2 GLU A 127 OE1 92.9 REMARK 620 3 ASP A 129 OD2 86.5 174.5 REMARK 620 4 ASP A 143 OD2 124.0 91.8 84.0 REMARK 620 5 HOH A 438 O 106.9 97.1 88.2 127.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CDP A 301 O3B REMARK 620 2 CDP A 301 O2A 85.9 REMARK 620 3 HOH A 409 O 171.6 89.7 REMARK 620 4 HOH A 412 O 105.7 80.8 80.7 REMARK 620 5 HOH A 421 O 84.7 168.0 100.5 94.6 REMARK 620 6 HOH A 444 O 83.4 92.9 89.7 168.4 93.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CDP A 301 O1B REMARK 620 2 CDP A 301 O1B 0.0 REMARK 620 3 HOH A 419 O 84.7 84.7 REMARK 620 4 HOH A 419 O 95.2 95.2 179.1 REMARK 620 5 HOH A 426 O 84.1 84.1 90.4 90.5 REMARK 620 6 HOH A 426 O 84.1 84.1 90.5 90.5 0.0 REMARK 620 7 HOH A 441 O 95.7 95.7 89.5 89.6 179.9 179.9 REMARK 620 8 HOH A 441 O 95.7 95.7 89.5 89.5 179.9 179.8 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CDP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 DBREF 5ZDN A 1 207 UNP D2SNF7 D2SNF7_STRFR 1 207 SEQADV 5ZDN GLY A -3 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDN SER A -2 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDN HIS A -1 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDN GLY A 0 UNP D2SNF7 EXPRESSION TAG SEQADV 5ZDN 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 CDP A 301 25 HET MG A 302 1 HET MG A 303 1 HET MG A 304 1 HET MG A 305 1 HET GOL A 306 6 HETNAM CDP CYTIDINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CDP C9 H15 N3 O11 P2 FORMUL 3 MG 4(MG 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *73(H2 O) HELIX 1 AA1 HIS A 66 GLY A 72 5 7 HELIX 2 AA2 ASP A 143 GLY A 154 1 12 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 ASP A 39 -1 N SER A 31 O THR A 55 SHEET 3 AA1 5 VAL A 17 LEU A 24 -1 N VAL A 18 O VAL A 34 SHEET 4 AA1 5 GLY A 120 THR A 123 1 O PHE A 121 N GLU A 19 SHEET 5 AA1 5 ARG A 115 ARG A 116 -1 N ARG A 115 O SER A 122 SHEET 1 AA2 8 THR A 55 PHE A 56 0 SHEET 2 AA2 8 ARG A 27 ASP A 39 -1 N SER A 31 O THR A 55 SHEET 3 AA2 8 VAL A 44 LEU A 48 -1 O HIS A 47 N ARG A 35 SHEET 4 AA2 8 ILE A 80 HIS A 84 -1 O GLN A 82 N VAL A 46 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 ASN A 109 N SER A 91 SHEET 7 AA2 8 ASP A 125 PRO A 133 -1 O VAL A 132 N TRP A 106 SHEET 8 AA2 8 ARG A 140 LYS A 142 -1 O LYS A 142 N ASP A 129 LINK OD1 ASN A 109 MG MG A 303 1555 1555 1.97 LINK OD2 ASP A 125 MG MG A 303 1555 1555 2.05 LINK O GLU A 127 MG MG A 302 1555 1555 2.06 LINK OE1 GLU A 127 MG MG A 302 1555 1555 1.93 LINK OD2 ASP A 129 MG MG A 302 1555 1555 2.11 LINK OD1 ASP A 129 MG MG A 303 1555 1555 2.03 LINK OD2 ASP A 143 MG MG A 302 1555 1555 2.05 LINK O3B CDP A 301 MG MG A 304 1555 1555 2.04 LINK O2A CDP A 301 MG MG A 304 1555 1555 2.22 LINK O1B CDP A 301 MG MG A 305 1555 1555 2.02 LINK O1B CDP A 301 MG MG A 305 1555 3655 2.02 LINK MG MG A 302 O HOH A 438 1555 1555 2.15 LINK MG MG A 303 O HOH A 402 1555 1555 2.22 LINK MG MG A 303 O HOH A 438 1555 1555 2.15 LINK MG MG A 303 O HOH A 450 1555 1555 2.20 LINK MG MG A 304 O HOH A 409 1555 1555 2.14 LINK MG MG A 304 O HOH A 412 1555 1555 1.80 LINK MG MG A 304 O HOH A 421 1555 1555 1.98 LINK MG MG A 304 O HOH A 444 1555 1555 2.34 LINK MG MG A 305 O HOH A 419 1555 1555 1.99 LINK MG MG A 305 O HOH A 419 1555 3655 1.99 LINK MG MG A 305 O HOH A 426 1555 1555 2.11 LINK MG MG A 305 O HOH A 426 1555 3655 2.11 LINK MG MG A 305 O HOH A 441 1555 1555 1.89 LINK MG MG A 305 O HOH A 441 1555 3655 1.89 CISPEP 1 ASP A 59 PRO A 60 0 -6.48 SITE 1 AC1 21 LEU A 54 TRP A 68 PHE A 71 ARG A 74 SITE 2 AC1 21 TRP A 75 GLN A 76 SER A 77 LYS A 142 SITE 3 AC1 21 LYS A 146 MG A 304 MG A 305 HOH A 409 SITE 4 AC1 21 HOH A 410 HOH A 412 HOH A 419 HOH A 421 SITE 5 AC1 21 HOH A 426 HOH A 427 HOH A 441 HOH A 444 SITE 6 AC1 21 HOH A 447 SITE 1 AC2 5 GLU A 127 ASP A 129 ASP A 143 HOH A 421 SITE 2 AC2 5 HOH A 438 SITE 1 AC3 6 ASN A 109 ASP A 125 ASP A 129 HOH A 402 SITE 2 AC3 6 HOH A 438 HOH A 450 SITE 1 AC4 5 CDP A 301 HOH A 409 HOH A 412 HOH A 421 SITE 2 AC4 5 HOH A 444 SITE 1 AC5 4 CDP A 301 HOH A 419 HOH A 426 HOH A 441 SITE 1 AC6 8 ARG A 20 ASP A 22 TYR A 32 HIS A 66 SITE 2 AC6 8 TRP A 68 ASP A 125 HOH A 409 HOH A 414 CRYST1 56.165 77.452 96.566 90.00 90.00 90.00 C 2 2 21 8 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 0.017805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012911 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010356 0.00000