HEADER HYDROLASE 24-JUN-14 4UQO TITLE RADA C-TERMINAL ATPASE DOMAIN FROM PYROCOCCUS FURIOSUS BOUND TO ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA REPAIR AND RECOMBINATION PROTEIN RADA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-349; COMPND 5 SYNONYM: RADA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS HYDROLASE, RADA, RECOMBINASE, ATPASE, ADP EXPDTA X-RAY DIFFRACTION AUTHOR M.E.MARSH,M.T.EHEBAUER,D.SCOTT,C.ABELL,T.L.BLUNDELL,M.HYVONEN REVDAT 4 10-JAN-24 4UQO 1 REMARK LINK REVDAT 3 27-JUL-16 4UQO 1 JRNL REVDAT 2 20-JUL-16 4UQO 1 JRNL REVDAT 1 14-JAN-15 4UQO 0 SPRSDE 14-JAN-15 4UQO 4A7O JRNL AUTH M.E.MARSH,D.E.SCOTT,M.T.EHEBAUER,C.ABELL,T.L.BLUNDELL, JRNL AUTH 2 M.HYVONEN JRNL TITL ATP HALF-SITES IN RADA AND RAD51 RECOMBINASES BIND JRNL TITL 2 NUCLEOTIDES JRNL REF FEBS OPEN BIO V. 6 372 2016 JRNL REFN ESSN 2211-5463 JRNL PMID 27419043 JRNL DOI 10.1002/2211-5463.12052 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0071 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 33051 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 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) : 1.88 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2307 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3472 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.85000 REMARK 3 B22 (A**2) : -2.06000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.34000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.529 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3623 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3573 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4906 ; 1.792 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8196 ; 1.087 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 6.184 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;34.121 ;23.780 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 652 ;13.909 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.171 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 563 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4066 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 823 ; 0.004 ; 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): 1795 ; 1.898 ; 1.937 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1794 ; 1.895 ; 1.937 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2243 ; 2.993 ; 2.888 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1828 ; 2.651 ; 2.321 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. RESIDUES A287-A306 AND B286-B304 ARE DISORDERED. REMARK 4 REMARK 4 4UQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1290061061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9728 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34773 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 43.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.510 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.47 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 4A6P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 60 MM NAPHOSPHATE PH 5.8, 15% PEG1000 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 43.56500 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MET A 107 REMARK 465 ALA A 287 REMARK 465 ASN A 288 REMARK 465 GLY A 301 REMARK 465 GLY A 302 REMARK 465 HIS A 303 REMARK 465 ILE A 304 REMARK 465 LEU A 305 REMARK 465 ALA A 306 REMARK 465 MET B 107 REMARK 465 GLN B 286 REMARK 465 ALA B 287 REMARK 465 ASN B 288 REMARK 465 GLY B 301 REMARK 465 GLY B 302 REMARK 465 HIS B 303 REMARK 465 ILE B 304 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 LEU B 214 O REMARK 470 LEU B 305 CG CD1 CD2 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 B 2224 O HOH B 2226 1.98 REMARK 500 N HIS A 307 O HOH A 2222 1.98 REMARK 500 O HOH B 2128 O HOH B 2197 2.06 REMARK 500 OE1 GLU B 180 O HOH B 2092 2.12 REMARK 500 N GLY A 336 O HOH A 2242 2.12 REMARK 500 O HOH B 2104 O HOH B 2105 2.12 REMARK 500 O HOH B 2192 O HOH B 2193 2.15 REMARK 500 NH1 ARG A 183 OD1 ASP A 194 2.16 REMARK 500 O HOH B 2074 O HOH B 2075 2.16 REMARK 500 O HOH A 2118 O HOH A 2119 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 192 CB - CG - OD1 ANGL. DEV. = 7.6 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 SER A 308 40.04 -101.65 REMARK 500 HIS B 307 177.50 179.98 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 A2003 DISTANCE = 6.99 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 MG A1351 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 145 OG1 REMARK 620 2 ADP A1350 O3B 92.6 REMARK 620 3 HOH A2041 O 90.1 89.5 REMARK 620 4 HOH A2042 O 90.4 176.6 89.0 REMARK 620 5 HOH A2043 O 89.0 93.9 176.5 87.7 REMARK 620 6 HOH A2218 O 178.7 88.0 91.1 88.9 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1351 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 145 OG1 REMARK 620 2 ADP B1350 O3B 89.6 REMARK 620 3 HOH B2041 O 90.6 174.1 REMARK 620 4 HOH B2042 O 81.6 86.2 88.0 REMARK 620 5 HOH B2043 O 90.1 91.6 94.3 171.4 REMARK 620 6 HOH B2195 O 170.3 84.9 94.0 90.0 98.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1352 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 212 O REMARK 620 2 ASP B 267 OD2 115.6 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 ADP B 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1351 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1352 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1353 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UPI RELATED DB: PDB REMARK 900 DIMERIC SULFATASE SPAS1 FROM SILICIBACTER POMEROYI REMARK 900 RELATED ID: 4UPK RELATED DB: PDB REMARK 900 PHOSPHONATE MONOESTER HYDROLASE SPPMH FROM SILICIBACTER POMEROYI REMARK 900 RELATED ID: 4UPL RELATED DB: PDB REMARK 900 DIMERIC SULFATASE SPAS2 FROM SILICIBACTER POMEROYI DBREF 4UQO A 108 349 UNP O74036 RADA_PYRFU 108 349 DBREF 4UQO B 108 349 UNP O74036 RADA_PYRFU 108 349 SEQADV 4UQO MET A 107 UNP O74036 EXPRESSION TAG SEQADV 4UQO ASN A 288 UNP O74036 ARG 288 ENGINEERED MUTATION SEQADV 4UQO A UNP O74036 PRO 289 DELETION SEQADV 4UQO A UNP O74036 ASP 290 DELETION SEQADV 4UQO A UNP O74036 ALA 291 DELETION SEQADV 4UQO A UNP O74036 PHE 292 DELETION SEQADV 4UQO A UNP O74036 PHE 293 DELETION SEQADV 4UQO A UNP O74036 GLY 294 DELETION SEQADV 4UQO A UNP O74036 ASP 295 DELETION SEQADV 4UQO A UNP O74036 PRO 296 DELETION SEQADV 4UQO A UNP O74036 THR 297 DELETION SEQADV 4UQO A UNP O74036 ARG 298 DELETION SEQADV 4UQO A UNP O74036 PRO 299 DELETION SEQADV 4UQO A UNP O74036 ILE 300 DELETION SEQADV 4UQO MET B 107 UNP O74036 EXPRESSION TAG SEQADV 4UQO ASN B 288 UNP O74036 ARG 288 ENGINEERED MUTATION SEQADV 4UQO B UNP O74036 PRO 289 DELETION SEQADV 4UQO B UNP O74036 ASP 290 DELETION SEQADV 4UQO B UNP O74036 ALA 291 DELETION SEQADV 4UQO B UNP O74036 PHE 292 DELETION SEQADV 4UQO B UNP O74036 PHE 293 DELETION SEQADV 4UQO B UNP O74036 GLY 294 DELETION SEQADV 4UQO B UNP O74036 ASP 295 DELETION SEQADV 4UQO B UNP O74036 PRO 296 DELETION SEQADV 4UQO B UNP O74036 THR 297 DELETION SEQADV 4UQO B UNP O74036 ARG 298 DELETION SEQADV 4UQO B UNP O74036 PRO 299 DELETION SEQADV 4UQO B UNP O74036 ILE 300 DELETION SEQRES 1 A 231 MET ALA THR ILE GLY ARG ILE SER THR GLY SER LYS SER SEQRES 2 A 231 LEU ASP LYS LEU LEU GLY GLY GLY ILE GLU THR GLN ALA SEQRES 3 A 231 ILE THR GLU VAL PHE GLY GLU PHE GLY SER GLY LYS THR SEQRES 4 A 231 GLN LEU ALA HIS THR LEU ALA VAL MET VAL GLN LEU PRO SEQRES 5 A 231 PRO GLU GLU GLY GLY LEU ASN GLY SER VAL ILE TRP ILE SEQRES 6 A 231 ASP THR GLU ASN THR PHE ARG PRO GLU ARG ILE ARG GLU SEQRES 7 A 231 ILE ALA GLN ASN ARG GLY LEU ASP PRO ASP GLU VAL LEU SEQRES 8 A 231 LYS HIS ILE TYR VAL ALA ARG ALA PHE ASN SER ASN HIS SEQRES 9 A 231 GLN MET LEU LEU VAL GLN GLN ALA GLU ASP LYS ILE LYS SEQRES 10 A 231 GLU LEU LEU ASN THR ASP ARG PRO VAL LYS LEU LEU ILE SEQRES 11 A 231 VAL ASP SER LEU THR SER HIS PHE ARG SER GLU TYR ILE SEQRES 12 A 231 GLY ARG GLY ALA LEU ALA GLU ARG GLN GLN LYS LEU ALA SEQRES 13 A 231 LYS HIS LEU ALA ASP LEU HIS ARG LEU ALA ASN LEU TYR SEQRES 14 A 231 ASP ILE ALA VAL PHE VAL THR ASN GLN VAL GLN ALA ASN SEQRES 15 A 231 GLY GLY HIS ILE LEU ALA HIS SER ALA THR LEU ARG VAL SEQRES 16 A 231 TYR LEU ARG LYS GLY LYS GLY GLY LYS ARG ILE ALA ARG SEQRES 17 A 231 LEU ILE ASP ALA PRO HIS LEU PRO GLU GLY GLU ALA VAL SEQRES 18 A 231 PHE SER ILE THR GLU LYS GLY ILE GLU ASP SEQRES 1 B 231 MET ALA THR ILE GLY ARG ILE SER THR GLY SER LYS SER SEQRES 2 B 231 LEU ASP LYS LEU LEU GLY GLY GLY ILE GLU THR GLN ALA SEQRES 3 B 231 ILE THR GLU VAL PHE GLY GLU PHE GLY SER GLY LYS THR SEQRES 4 B 231 GLN LEU ALA HIS THR LEU ALA VAL MET VAL GLN LEU PRO SEQRES 5 B 231 PRO GLU GLU GLY GLY LEU ASN GLY SER VAL ILE TRP ILE SEQRES 6 B 231 ASP THR GLU ASN THR PHE ARG PRO GLU ARG ILE ARG GLU SEQRES 7 B 231 ILE ALA GLN ASN ARG GLY LEU ASP PRO ASP GLU VAL LEU SEQRES 8 B 231 LYS HIS ILE TYR VAL ALA ARG ALA PHE ASN SER ASN HIS SEQRES 9 B 231 GLN MET LEU LEU VAL GLN GLN ALA GLU ASP LYS ILE LYS SEQRES 10 B 231 GLU LEU LEU ASN THR ASP ARG PRO VAL LYS LEU LEU ILE SEQRES 11 B 231 VAL ASP SER LEU THR SER HIS PHE ARG SER GLU TYR ILE SEQRES 12 B 231 GLY ARG GLY ALA LEU ALA GLU ARG GLN GLN LYS LEU ALA SEQRES 13 B 231 LYS HIS LEU ALA ASP LEU HIS ARG LEU ALA ASN LEU TYR SEQRES 14 B 231 ASP ILE ALA VAL PHE VAL THR ASN GLN VAL GLN ALA ASN SEQRES 15 B 231 GLY GLY HIS ILE LEU ALA HIS SER ALA THR LEU ARG VAL SEQRES 16 B 231 TYR LEU ARG LYS GLY LYS GLY GLY LYS ARG ILE ALA ARG SEQRES 17 B 231 LEU ILE ASP ALA PRO HIS LEU PRO GLU GLY GLU ALA VAL SEQRES 18 B 231 PHE SER ILE THR GLU LYS GLY ILE GLU ASP HET ADP A1350 27 HET MG A1351 1 HET NA A1352 1 HET ADP B1350 27 HET MG B1351 1 HET NA B1352 1 HET NA B1353 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION FORMUL 3 ADP 2(C10 H15 N5 O10 P2) FORMUL 4 MG 2(MG 2+) FORMUL 5 NA 3(NA 1+) FORMUL 10 HOH *496(H2 O) HELIX 1 1 SER A 117 LEU A 124 1 8 HELIX 2 2 GLY A 143 VAL A 155 1 13 HELIX 3 3 PRO A 158 GLY A 162 5 5 HELIX 4 4 ARG A 178 ARG A 189 1 12 HELIX 5 5 ASP A 192 HIS A 199 1 8 HELIX 6 6 ASN A 207 LEU A 226 1 20 HELIX 7 7 THR A 241 TYR A 248 1 8 HELIX 8 8 GLY A 252 ASP A 276 1 25 HELIX 9 9 LYS A 319 GLY A 321 5 3 HELIX 10 10 SER B 117 GLY B 125 1 9 HELIX 11 11 GLY B 143 VAL B 155 1 13 HELIX 12 12 PRO B 158 GLY B 162 5 5 HELIX 13 13 ARG B 178 ARG B 189 1 12 HELIX 14 14 ASP B 192 HIS B 199 1 8 HELIX 15 15 ASN B 207 LEU B 213 1 7 HELIX 16 16 VAL B 215 LEU B 226 1 12 HELIX 17 17 THR B 241 TYR B 248 1 8 HELIX 18 18 GLY B 252 TYR B 275 1 24 HELIX 19 19 LYS B 319 GLY B 321 5 3 SHEET 1 AA 2 ARG A 112 ILE A 113 0 SHEET 2 AA 2 ILE A 128 GLU A 129 -1 O ILE A 128 N ILE A 113 SHEET 1 AB 9 ILE A 200 ARG A 204 0 SHEET 2 AB 9 SER A 167 ASP A 172 1 O VAL A 168 N TYR A 201 SHEET 3 AB 9 VAL A 232 ASP A 238 1 N LYS A 233 O SER A 167 SHEET 4 AB 9 ALA A 278 GLN A 284 1 O ALA A 278 N LEU A 235 SHEET 5 AB 9 ALA A 132 GLY A 138 1 O ALA A 132 N VAL A 279 SHEET 6 AB 9 LEU A 311 LYS A 317 1 O LEU A 311 N GLU A 135 SHEET 7 AB 9 ARG A 323 ILE A 328 -1 O ILE A 324 N ARG A 316 SHEET 8 AB 9 ALA A 338 THR A 343 -1 O ALA A 338 N ALA A 325 SHEET 9 AB 9 GLY A 346 GLU A 348 -1 O GLY A 346 N THR A 343 SHEET 1 BA 2 ARG B 112 ILE B 113 0 SHEET 2 BA 2 ILE B 128 GLU B 129 -1 O ILE B 128 N ILE B 113 SHEET 1 BB 9 ILE B 200 ARG B 204 0 SHEET 2 BB 9 SER B 167 ASP B 172 1 O VAL B 168 N TYR B 201 SHEET 3 BB 9 VAL B 232 ASP B 238 1 N LYS B 233 O SER B 167 SHEET 4 BB 9 ALA B 278 GLN B 284 1 O ALA B 278 N LEU B 235 SHEET 5 BB 9 ALA B 132 GLY B 138 1 O ALA B 132 N VAL B 279 SHEET 6 BB 9 LEU B 311 LYS B 317 1 O LEU B 311 N GLU B 135 SHEET 7 BB 9 ARG B 323 ILE B 328 -1 O ILE B 324 N ARG B 316 SHEET 8 BB 9 ALA B 338 THR B 343 -1 O ALA B 338 N ALA B 325 SHEET 9 BB 9 GLY B 346 GLU B 348 -1 O GLY B 346 N THR B 343 LINK OG1 THR A 145 MG MG A1351 1555 1555 1.97 LINK O3B ADP A1350 MG MG A1351 1555 1555 2.04 LINK MG MG A1351 O HOH A2041 1555 1555 2.06 LINK MG MG A1351 O HOH A2042 1555 1555 1.96 LINK MG MG A1351 O HOH A2043 1555 1555 2.06 LINK MG MG A1351 O HOH A2218 1555 1555 2.07 LINK NA NA A1352 O HOH A2260 1555 1555 3.05 LINK OG1 THR B 145 MG MG B1351 1555 1555 2.10 LINK O MET B 212 NA NA B1352 1555 1555 3.17 LINK OD2 ASP B 267 NA NA B1352 1555 1555 2.71 LINK O3B ADP B1350 MG MG B1351 1555 1555 2.09 LINK MG MG B1351 O HOH B2041 1555 1555 2.01 LINK MG MG B1351 O HOH B2042 1555 1555 2.05 LINK MG MG B1351 O HOH B2043 1555 1555 2.05 LINK MG MG B1351 O HOH B2195 1555 1555 1.99 CISPEP 1 ASP A 238 SER A 239 0 0.07 CISPEP 2 ASP B 238 SER B 239 0 2.94 SITE 1 AC1 23 GLU B 139 PHE B 140 GLY B 141 SER B 142 SITE 2 AC1 23 GLY B 143 LYS B 144 THR B 145 GLN B 146 SITE 3 AC1 23 ARG B 181 GLN B 284 ARG B 323 ILE B 342 SITE 4 AC1 23 MG B1351 HOH B2042 HOH B2043 HOH B2044 SITE 5 AC1 23 HOH B2096 HOH B2100 HOH B2101 HOH B2195 SITE 6 AC1 23 HOH B2224 HOH B2233 HOH B2236 SITE 1 AC2 6 THR B 145 ADP B1350 HOH B2041 HOH B2042 SITE 2 AC2 6 HOH B2043 HOH B2195 SITE 1 AC3 23 PHE A 140 GLY A 141 SER A 142 GLY A 143 SITE 2 AC3 23 LYS A 144 THR A 145 GLN A 146 ARG A 181 SITE 3 AC3 23 GLN A 284 ARG A 323 ILE A 342 MG A1351 SITE 4 AC3 23 HOH A2041 HOH A2043 HOH A2045 HOH A2101 SITE 5 AC3 23 HOH A2102 HOH A2110 HOH A2218 HOH A2234 SITE 6 AC3 23 HOH A2247 HOH A2256 HOH A2257 SITE 1 AC4 6 THR A 145 ADP A1350 HOH A2041 HOH A2042 SITE 2 AC4 6 HOH A2043 HOH A2218 SITE 1 AC5 4 GLY A 111 ARG A 112 LEU A 164 HOH A2260 SITE 1 AC6 4 MET B 212 VAL B 215 HIS B 264 ASP B 267 SITE 1 AC7 4 PHE B 206 ARG B 316 GLY B 318 LYS B 319 CRYST1 40.308 87.130 62.322 90.00 90.55 90.00 P 1 21 1 4 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 0.024809 0.000000 0.000238 0.00000 SCALE2 0.000000 0.011477 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016046 0.00000 MTRIX1 1 -1.000000 0.004410 -0.000132 20.07000 1 MTRIX2 1 -0.004410 -1.000000 0.005209 23.98000 1 MTRIX3 1 -0.000109 0.005210 1.000000 -31.19000 1