HEADER OXIDOREDUCTASE 15-APR-09 3H2Z TITLE THE CRYSTAL STRUCTURE OF MANNITOL-1-PHOSPHATE DEHYDROGENASE FROM TITLE 2 SHIGELLA FLEXNERI COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNITOL-1-PHOSPHATE 5-DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.17; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI 2A STR. 2457T; SOURCE 3 ORGANISM_TAXID: 198215; SOURCE 4 STRAIN: TAXON:198215; SOURCE 5 GENE: MTLD, S4134, SF3634; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDM68 KEYWDS MMANNITOL-1-PHOSPHATE DEHYDROGENASE, SHIGELLA FLEXNERI, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, STRUCTURAL GENOMICS, MIDWEST CENTER KEYWDS 3 FOR STRUCTURAL GENOMICS (MCSG), NAD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.WU,S.CLANCY,A.JOACHIMIAK,MIDWEST CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (MCSG) REVDAT 3 13-JUL-11 3H2Z 1 VERSN REVDAT 2 08-DEC-10 3H2Z 1 TITLE REVDAT 1 16-JUN-09 3H2Z 0 JRNL AUTH R.WU,S.CLANCY,A.JOACHIMIAK JRNL TITL THE CRYSTAL STRUCTURE OF MANNITOL-1-PHOSPHATE DEHYDROGENASE JRNL TITL 2 FROM SHIGELLA FLEXNERI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0054 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 39865 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2125 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.38 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2862 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 25.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.70000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : -1.40000 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): 0.117 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.012 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3017 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4098 ; 1.457 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 5.411 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;37.202 ;24.962 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 525 ;13.878 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.621 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 472 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2263 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1921 ; 0.823 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3082 ; 1.494 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1096 ; 2.700 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1008 ; 4.247 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 382 REMARK 3 ORIGIN FOR THE GROUP (A): 30.5219 66.2399 12.3719 REMARK 3 T TENSOR REMARK 3 T11: 0.0209 T22: 0.0513 REMARK 3 T33: 0.0350 T12: 0.0267 REMARK 3 T13: -0.0028 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.1643 L22: 0.6869 REMARK 3 L33: 0.8311 L12: 0.1057 REMARK 3 L13: 0.0084 L23: 0.2196 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: 0.0150 S13: -0.0089 REMARK 3 S21: 0.0490 S22: 0.0137 S23: -0.0525 REMARK 3 S31: 0.0550 S32: 0.1209 S33: -0.0109 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 REMARK 4 REMARK 4 3H2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-09. REMARK 100 THE RCSB ID CODE IS RCSB052626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : SI 111, CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 17.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 52.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.87400 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 61.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA ACETATE, PH 5.5, 1.4M REMARK 280 NACITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 75.54600 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 46.08950 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 75.54600 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 46.08950 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 75.54600 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 46.08950 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 75.54600 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 46.08950 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 75.54600 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 46.08950 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 75.54600 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 46.08950 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 75.54600 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 46.08950 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 75.54600 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 75.54600 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 46.08950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -139.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 151.09200 REMARK 350 BIOMT3 2 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 SER A 164 REMARK 465 ALA A 165 REMARK 465 SER A 166 REMARK 465 ALA A 167 REMARK 465 THR A 168 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 ASN A 169 CG OD1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 289 CG 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 NH1 ARG A 94 O2 PO4 A 396 1.97 REMARK 500 O HOH A 497 O HOH A 508 2.07 REMARK 500 N MSE A 1 O HOH A 485 2.13 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 125 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 PRO A 320 CB - CA - C ANGL. DEV. = -13.6 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 ALA A 8 42.96 -95.32 REMARK 500 PHE A 15 -73.98 -134.92 REMARK 500 HIS A 44 11.11 53.07 REMARK 500 THR A 215 -67.20 -122.11 REMARK 500 ASP A 305 -164.61 -102.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 502 DISTANCE = 5.53 ANGSTROMS 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 NA A 387 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 266 OD2 REMARK 620 2 HOH A 651 O 87.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 389 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 498 O REMARK 620 2 HOH A 497 O 138.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 390 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 477 O REMARK 620 2 HOH A 633 O 80.1 REMARK 620 3 HOH A 503 O 82.3 79.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 392 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 638 O REMARK 620 2 HOH A 508 O 100.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 387 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 390 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 392 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 393 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 394 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 395 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 396 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC28246 RELATED DB: TARGETDB DBREF 3H2Z A 1 382 UNP Q83PQ0 MTLD_SHIFL 1 382 SEQRES 1 A 382 MSE LYS ALA LEU HIS PHE GLY ALA GLY ASN ILE GLY ARG SEQRES 2 A 382 GLY PHE ILE GLY LYS LEU LEU ALA ASP ALA GLY ILE GLN SEQRES 3 A 382 LEU THR PHE ALA ASP VAL ASN GLN VAL VAL LEU ASP ALA SEQRES 4 A 382 LEU ASN ALA ARG HIS SER TYR GLN VAL HIS VAL VAL GLY SEQRES 5 A 382 GLU THR GLU GLN VAL ASP THR VAL SER GLY VAL ASN ALA SEQRES 6 A 382 VAL SER SER ILE GLY ASP ASP VAL VAL ASP LEU ILE ALA SEQRES 7 A 382 GLN VAL ASP LEU VAL THR THR ALA VAL GLY PRO VAL VAL SEQRES 8 A 382 LEU GLU ARG ILE ALA PRO ALA ILE ALA LYS GLY LEU VAL SEQRES 9 A 382 LYS ARG LYS GLU GLN GLY ASN GLU SER PRO LEU ASN ILE SEQRES 10 A 382 ILE ALA CYS GLU ASN MSE VAL ARG GLY THR THR GLN LEU SEQRES 11 A 382 LYS GLY HIS VAL MSE ASN ALA LEU PRO GLU ASP ALA LYS SEQRES 12 A 382 ALA TRP VAL GLU GLU HIS VAL GLY PHE VAL ASP SER ALA SEQRES 13 A 382 VAL ASP ARG ILE VAL PRO PRO SER ALA SER ALA THR ASN SEQRES 14 A 382 ASP PRO LEU GLU VAL THR VAL GLU THR PHE SER GLU TRP SEQRES 15 A 382 ILE VAL ASP LYS THR GLN PHE LYS GLY ALA LEU PRO ASN SEQRES 16 A 382 ILE PRO GLY MSE GLU LEU THR ASP ASN LEU MSE ALA PHE SEQRES 17 A 382 VAL GLU ARG LYS LEU PHE THR LEU ASN THR GLY HIS ALA SEQRES 18 A 382 ILE THR ALA TYR LEU GLY LYS LEU ALA GLY HIS GLN THR SEQRES 19 A 382 ILE ARG ASP ALA ILE LEU ASP GLU LYS ILE ARG ALA VAL SEQRES 20 A 382 VAL LYS GLY ALA MSE GLU GLU SER GLY ALA VAL LEU ILE SEQRES 21 A 382 LYS ARG TYR GLY PHE ASP ALA ASP LYS HIS ALA ALA TYR SEQRES 22 A 382 ILE GLN LYS ILE LEU GLY ARG PHE GLU ASN PRO TYR LEU SEQRES 23 A 382 LYS ASP ASP VAL GLU ARG VAL GLY ARG GLN PRO LEU ARG SEQRES 24 A 382 LYS LEU SER ALA GLY ASP ARG LEU ILE LYS PRO LEU LEU SEQRES 25 A 382 GLY THR LEU GLU TYR SER LEU PRO HIS LYS ASN LEU ILE SEQRES 26 A 382 GLN GLY ILE ALA GLY ALA MSE HIS PHE ARG SER GLU ASP SEQRES 27 A 382 ASP PRO GLN ALA GLN GLU LEU ALA ALA LEU ILE ALA ASP SEQRES 28 A 382 LYS GLY PRO GLN ALA ALA LEU ALA GLN ILE SER GLY LEU SEQRES 29 A 382 ASP ALA ASN SER GLU VAL VAL SER GLU ALA VAL THR ALA SEQRES 30 A 382 TYR LYS ALA MSE GLN MODRES 3H2Z MSE A 1 MET SELENOMETHIONINE MODRES 3H2Z MSE A 123 MET SELENOMETHIONINE MODRES 3H2Z MSE A 135 MET SELENOMETHIONINE MODRES 3H2Z MSE A 199 MET SELENOMETHIONINE MODRES 3H2Z MSE A 206 MET SELENOMETHIONINE MODRES 3H2Z MSE A 252 MET SELENOMETHIONINE MODRES 3H2Z MSE A 332 MET SELENOMETHIONINE MODRES 3H2Z MSE A 381 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 123 8 HET MSE A 135 8 HET MSE A 199 8 HET MSE A 206 8 HET MSE A 252 8 HET MSE A 332 8 HET MSE A 381 8 HET ACT A 383 4 HET ACT A 384 4 HET ACT A 385 4 HET GOL A 386 6 HET NA A 387 1 HET ACT A 388 4 HET NA A 389 1 HET NA A 390 1 HET NA A 391 1 HET NA A 392 1 HET PO4 A 393 5 HET PO4 A 394 5 HET PO4 A 395 5 HET PO4 A 396 5 HETNAM MSE SELENOMETHIONINE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 ACT 4(C2 H3 O2 1-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 NA 5(NA 1+) FORMUL 12 PO4 4(O4 P 3-) FORMUL 16 HOH *255(H2 O) HELIX 1 1 GLY A 9 PHE A 15 1 7 HELIX 2 2 PHE A 15 ALA A 23 1 9 HELIX 3 3 ASN A 33 HIS A 44 1 12 HELIX 4 4 ASP A 71 ALA A 78 1 8 HELIX 5 5 GLY A 88 ILE A 95 1 8 HELIX 6 6 ILE A 95 GLY A 110 1 16 HELIX 7 7 ARG A 125 ASN A 136 1 12 HELIX 8 8 ALA A 137 LEU A 138 5 2 HELIX 9 9 PRO A 139 ASP A 141 5 3 HELIX 10 10 ALA A 142 HIS A 149 1 8 HELIX 11 11 THR A 187 PHE A 189 5 3 HELIX 12 12 ASN A 204 THR A 215 1 12 HELIX 13 13 THR A 215 ALA A 230 1 16 HELIX 14 14 THR A 234 LEU A 240 1 7 HELIX 15 15 ASP A 241 GLY A 264 1 24 HELIX 16 16 ASP A 266 GLU A 282 1 17 HELIX 17 17 ASP A 289 GLY A 294 1 6 HELIX 18 18 GLN A 296 LEU A 301 1 6 HELIX 19 19 LEU A 307 SER A 318 1 12 HELIX 20 20 HIS A 321 HIS A 333 1 13 HELIX 21 21 ASP A 339 GLY A 363 1 25 HELIX 22 22 SER A 368 MSE A 381 1 14 SHEET 1 A 6 ASN A 64 SER A 67 0 SHEET 2 A 6 GLN A 26 ASP A 31 1 N PHE A 29 O ASN A 64 SHEET 3 A 6 LYS A 2 PHE A 6 1 N HIS A 5 O THR A 28 SHEET 4 A 6 LEU A 82 THR A 85 1 O THR A 84 N PHE A 6 SHEET 5 A 6 LEU A 115 ALA A 119 1 O ILE A 118 N VAL A 83 SHEET 6 A 6 VAL A 150 VAL A 153 1 O GLY A 151 N ILE A 117 SHEET 1 B 3 GLU A 55 SER A 61 0 SHEET 2 B 3 SER A 45 VAL A 51 -1 N VAL A 48 O ASP A 58 SHEET 3 B 3 VAL A 174 GLU A 177 1 O VAL A 176 N VAL A 51 SHEET 1 C 3 SER A 155 ASP A 158 0 SHEET 2 C 3 GLU A 181 ASP A 185 -1 O ILE A 183 N ALA A 156 SHEET 3 C 3 MSE A 199 THR A 202 1 O GLU A 200 N TRP A 182 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ASN A 122 N MSE A 123 1555 1555 1.33 LINK C MSE A 123 N VAL A 124 1555 1555 1.33 LINK C VAL A 134 N MSE A 135 1555 1555 1.34 LINK C MSE A 135 N ASN A 136 1555 1555 1.33 LINK C GLY A 198 N MSE A 199 1555 1555 1.33 LINK C MSE A 199 N GLU A 200 1555 1555 1.33 LINK C LEU A 205 N MSE A 206 1555 1555 1.34 LINK C MSE A 206 N ALA A 207 1555 1555 1.34 LINK C ALA A 251 N MSE A 252 1555 1555 1.34 LINK C MSE A 252 N GLU A 253 1555 1555 1.33 LINK C ALA A 331 N MSE A 332 1555 1555 1.33 LINK C MSE A 332 N HIS A 333 1555 1555 1.33 LINK C ALA A 380 N MSE A 381 1555 1555 1.33 LINK C MSE A 381 N GLN A 382 1555 1555 1.33 LINK OD2 ASP A 266 NA NA A 387 1555 1555 2.10 LINK NA NA A 387 O HOH A 651 1555 1555 2.31 LINK NA NA A 389 O HOH A 498 1555 1555 2.32 LINK NA NA A 389 O HOH A 497 1555 1555 2.20 LINK NA NA A 390 O HOH A 477 1555 1555 2.41 LINK NA NA A 390 O HOH A 633 1555 1555 2.40 LINK NA NA A 390 O HOH A 503 1555 1555 2.31 LINK NA NA A 392 O HOH A 638 1555 1555 2.61 LINK NA NA A 392 O HOH A 508 1555 1555 2.13 SITE 1 AC1 5 ASN A 10 ILE A 11 HOH A 529 HOH A 575 SITE 2 AC1 5 HOH A 618 SITE 1 AC2 4 PHE A 265 ASP A 266 LYS A 269 HOH A 446 SITE 1 AC3 4 MSE A 123 VAL A 124 GLN A 129 GOL A 386 SITE 1 AC4 7 GLU A 93 ASN A 136 SER A 302 GLY A 304 SITE 2 AC4 7 ASP A 305 ACT A 385 HOH A 522 SITE 1 AC5 3 ASP A 266 HOH A 481 HOH A 651 SITE 1 AC6 3 LYS A 186 THR A 187 HOH A 651 SITE 1 AC7 2 HOH A 497 HOH A 498 SITE 1 AC8 3 HOH A 477 HOH A 503 HOH A 633 SITE 1 AC9 2 LYS A 18 ARG A 159 SITE 1 BC1 4 GLU A 369 VAL A 370 HOH A 508 HOH A 638 SITE 1 BC2 5 ASN A 122 ARG A 299 LYS A 300 ARG A 306 SITE 2 BC2 5 HOH A 510 SITE 1 BC3 4 ARG A 245 LYS A 249 GLN A 275 HOH A 475 SITE 1 BC4 4 THR A 202 ASP A 203 ASN A 204 LYS A 269 SITE 1 BC5 9 GLY A 7 ALA A 30 ASP A 31 VAL A 32 SITE 2 BC5 9 SER A 68 VAL A 91 ARG A 94 ILE A 95 SITE 3 BC5 9 HOH A 486 CRYST1 151.092 151.092 92.179 90.00 90.00 90.00 I 4 2 2 16 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 0.006618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006618 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010848 0.00000 HETATM 1 N MSE A 1 17.703 43.918 5.608 1.00 21.73 N HETATM 2 CA MSE A 1 18.013 45.247 4.965 1.00 22.24 C HETATM 3 C MSE A 1 19.448 45.302 4.465 1.00 20.58 C HETATM 4 O MSE A 1 20.327 44.586 4.961 1.00 18.63 O HETATM 5 CB MSE A 1 17.765 46.394 5.932 1.00 23.05 C HETATM 6 CG MSE A 1 16.323 46.518 6.285 1.00 29.24 C HETATM 7 SE MSE A 1 15.729 48.323 6.112 0.40 36.63 SE HETATM 8 CE MSE A 1 17.221 49.293 6.972 1.00 27.16 C