HEADER HYDROLASE 28-MAR-12 4EEK TITLE CRYSTAL STRUCTURE OF HAD FAMILY HYDROLASE DR_1622 FROM DEINOCOCCUS TITLE 2 RADIODURANS R1 (TARGET EFI-501256) WITH BOUND PHOSPHATE AND SODIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-PHOSPHOGLUCOMUTASE-RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 1299; SOURCE 4 GENE: DR_1622; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, MAGNESIUM BINDING SITE, ENZYME FUNCTION INITIATIVE, KEYWDS 2 STRUCTURAL GENOMICS EXPDTA X-RAY DIFFRACTION AUTHOR Y.PATSKOVSKY,R.TORO,R.BHOSLE,B.HILLERICH,R.D.SEIDEL,E.WASHINGTON, AUTHOR 2 A.SCOTT GLENN,S.CHOWDHURY,B.EVANS,J.HAMMONDS,W.D.ZENCHECK,H.J.IMKER, AUTHOR 3 J.A.GERLT,K.N.ALLEN,D.DUNAWAY-MARIANO,S.C.ALMO,ENZYME FUNCTION AUTHOR 4 INITIATIVE (EFI) REVDAT 3 13-SEP-23 4EEK 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 4EEK 1 AUTHOR REVDAT 1 18-APR-12 4EEK 0 JRNL AUTH Y.PATSKOVSKY,R.TORO,R.BHOSLE,B.HILLERICH,R.D.SEIDEL, JRNL AUTH 2 E.WASHINGTON,A.SCOTT GLENN,S.CHOWDHURY,B.EVANS,J.HAMMONDS, JRNL AUTH 3 W.D.ZENCHECK,H.J.IMKER,K.N.ALLEN,D.DUNAWAY-MARIANO, JRNL AUTH 4 J.A.GERLT,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF HAD HYDROLASE DR_1622 DEINOCOCCUS JRNL TITL 2 RADIODURANS R1 (TARGET EFI-501256) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 33070 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1080 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2049 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1703 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 182 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : -0.28000 REMARK 3 B33 (A**2) : 0.42000 REMARK 3 B12 (A**2) : -0.14000 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): 0.088 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.727 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 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): 1815 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2494 ; 1.483 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 250 ; 5.064 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;34.889 ;23.165 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 272 ;14.550 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.003 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 286 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1416 ; 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4EEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000071518. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39048 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 22.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 18.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2FDR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HYDROGEN PHOSPHATE, 0.1M REMARK 280 CITRIC ACID, PH 4.2, 40% PEG 300, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 182.06267 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 91.03133 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 136.54700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 45.51567 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 227.57833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 182.06267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 91.03133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 45.51567 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 136.54700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 227.57833 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: 2840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HOH A 467 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 MET A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 232 REMARK 465 THR A 233 REMARK 465 PRO A 234 REMARK 465 ASP A 235 REMARK 465 LEU A 236 REMARK 465 SER A 237 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 LEU A 13 -70.01 -93.90 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 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD2 REMARK 620 2 ASP A 14 O 81.8 REMARK 620 3 ASP A 171 OD1 88.2 94.3 REMARK 620 4 PO4 A 301 O4 86.1 93.1 169.9 REMARK 620 5 HOH A 402 O 155.5 105.8 113.9 70.4 REMARK 620 6 HOH A 403 O 84.9 164.6 93.1 78.1 83.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4EEN RELATED DB: PDB REMARK 900 STRUCTURE OF HAD FAMILY HYDROLASE DR_1622 WITH BOUND MAGNESIUM REMARK 900 RELATED ID: 4EEL RELATED DB: PDB REMARK 900 STRUCTURE OF HAD FAMILY HYDROLASE DR_1622 WITH BOUND CITRATE AND REMARK 900 SODIUM REMARK 900 RELATED ID: EFI-501256 RELATED DB: TARGETTRACK DBREF 4EEK A 1 237 UNP Q9RTX8 Q9RTX8_DEIRA 1 237 SEQADV 4EEK MET A -21 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -20 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -19 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -18 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -17 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -16 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK HIS A -15 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK SER A -14 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK SER A -13 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK GLY A -12 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK VAL A -11 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK ASP A -10 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK LEU A -9 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK GLY A -8 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK THR A -7 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK GLU A -6 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK ASN A -5 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK LEU A -4 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK TYR A -3 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK PHE A -2 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK GLN A -1 UNP Q9RTX8 EXPRESSION TAG SEQADV 4EEK SER A 0 UNP Q9RTX8 EXPRESSION TAG SEQRES 1 A 259 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 259 GLY THR GLU ASN LEU TYR PHE GLN SER MET PRO ASP ALA SEQRES 3 A 259 PRO PHE ASP ALA VAL LEU PHE ASP LEU ASP GLY VAL LEU SEQRES 4 A 259 VAL GLU SER GLU GLY ILE ILE ALA GLN VAL TRP GLN SER SEQRES 5 A 259 VAL LEU ALA GLU ARG GLY LEU HIS LEU ASP LEU THR GLU SEQRES 6 A 259 ILE ALA MET TYR PHE THR GLY GLN ARG PHE ASP GLY VAL SEQRES 7 A 259 LEU ALA TYR LEU ALA GLN GLN HIS ASP PHE VAL PRO PRO SEQRES 8 A 259 PRO ASP PHE LEU ASP VAL LEU GLU THR ARG PHE ASN ALA SEQRES 9 A 259 ALA MET THR GLY VAL THR ALA ILE GLU GLY ALA ALA GLU SEQRES 10 A 259 THR LEU ARG ALA LEU ARG ALA ALA GLY VAL PRO PHE ALA SEQRES 11 A 259 ILE GLY SER ASN SER GLU ARG GLY ARG LEU HIS LEU LYS SEQRES 12 A 259 LEU ARG VAL ALA GLY LEU THR GLU LEU ALA GLY GLU HIS SEQRES 13 A 259 ILE TYR ASP PRO SER TRP VAL GLY GLY ARG GLY LYS PRO SEQRES 14 A 259 HIS PRO ASP LEU TYR THR PHE ALA ALA GLN GLN LEU GLY SEQRES 15 A 259 ILE LEU PRO GLU ARG CYS VAL VAL ILE GLU ASP SER VAL SEQRES 16 A 259 THR GLY GLY ALA ALA GLY LEU ALA ALA GLY ALA THR LEU SEQRES 17 A 259 TRP GLY LEU LEU VAL PRO GLY HIS PRO HIS PRO ASP GLY SEQRES 18 A 259 ALA ALA ALA LEU SER ARG LEU GLY ALA ALA ARG VAL LEU SEQRES 19 A 259 THR SER HIS ALA GLU LEU ARG ALA ALA LEU ALA GLU ALA SEQRES 20 A 259 GLY LEU LEU THR PRO ALA LEU THR PRO ASP LEU SER HET PO4 A 301 5 HET NA A 302 1 HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION FORMUL 2 PO4 O4 P 3- FORMUL 3 NA NA 1+ FORMUL 4 HOH *182(H2 O) HELIX 1 1 SER A 20 ARG A 35 1 16 HELIX 2 2 ASP A 40 PHE A 48 1 9 HELIX 3 3 ARG A 52 ASP A 65 1 14 HELIX 4 4 ASP A 71 THR A 85 1 15 HELIX 5 5 GLY A 92 GLY A 104 1 13 HELIX 6 6 GLU A 114 ALA A 125 1 12 HELIX 7 7 LEU A 127 GLY A 132 1 6 HELIX 8 8 ASP A 137 GLY A 142 5 6 HELIX 9 9 PRO A 149 LEU A 159 1 11 HELIX 10 10 LEU A 162 GLU A 164 5 3 HELIX 11 11 SER A 172 GLY A 183 1 12 HELIX 12 12 GLY A 199 GLY A 207 1 9 HELIX 13 13 SER A 214 ALA A 225 1 12 SHEET 1 A 6 ILE A 135 TYR A 136 0 SHEET 2 A 6 PHE A 107 GLY A 110 1 N ILE A 109 O TYR A 136 SHEET 3 A 6 ALA A 8 ASP A 12 1 N PHE A 11 O ALA A 108 SHEET 4 A 6 CYS A 166 GLU A 170 1 O VAL A 167 N LEU A 10 SHEET 5 A 6 THR A 185 LEU A 189 1 O THR A 185 N VAL A 168 SHEET 6 A 6 ARG A 210 LEU A 212 1 O LEU A 212 N GLY A 188 SHEET 1 B 2 VAL A 18 GLU A 19 0 SHEET 2 B 2 THR A 88 ALA A 89 -1 O THR A 88 N GLU A 19 LINK OD2 ASP A 12 NA NA A 302 1555 1555 2.37 LINK O ASP A 14 NA NA A 302 1555 1555 2.31 LINK OD1 ASP A 171 NA NA A 302 1555 1555 2.26 LINK O4 PO4 A 301 NA NA A 302 1555 1555 2.54 LINK NA NA A 302 O HOH A 402 1555 1555 2.38 LINK NA NA A 302 O HOH A 403 1555 1555 2.41 CISPEP 1 LYS A 146 PRO A 147 0 10.40 SITE 1 AC1 10 ASP A 12 LEU A 13 ASP A 14 SER A 111 SITE 2 AC1 10 ASN A 112 LYS A 146 NA A 302 HOH A 402 SITE 3 AC1 10 HOH A 404 HOH A 520 SITE 1 AC2 6 ASP A 12 ASP A 14 ASP A 171 PO4 A 301 SITE 2 AC2 6 HOH A 402 HOH A 403 CRYST1 55.537 55.537 273.094 90.00 90.00 120.00 P 65 2 2 12 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 0.018006 0.010396 0.000000 0.00000 SCALE2 0.000000 0.020792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003662 0.00000