HEADER HYDROLASE 18-APR-11 2YGK TITLE CRYSTAL STRUCTURE OF THE NURA NUCLEASE FROM SULFOLOBUS SOLFATARICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NURA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)ROSETTA; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS HYDROLASE, DNA REPAIR, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR N.J.RZECHORZEK,J.K.BLACKWOOD,A.S.ABRAMS,J.D.MAMAN,N.P.ROBINSON, AUTHOR 2 L.PELLEGRINI REVDAT 3 09-OCT-24 2YGK 1 REMARK LINK REVDAT 2 25-APR-12 2YGK 1 JRNL REVDAT 1 14-DEC-11 2YGK 0 JRNL AUTH J.K.BLACKWOOD,N.J.RZECHORZEK,A.S.ABRAMS,J.D.MAMAN, JRNL AUTH 2 L.PELLEGRINI,N.P.ROBINSON JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-END PROCESSING JRNL TITL 2 BY THE ARCHAEAL HERA HELICASE-NURA NUCLEASE COMPLEX. JRNL REF NUCLEIC ACIDS RES. V. 40 3183 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22135300 JRNL DOI 10.1093/NAR/GKR1157 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22842 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1230 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1662 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : -2.00000 REMARK 3 B33 (A**2) : 1.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.010 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.331 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.286 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.798 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5258 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3738 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7050 ; 1.395 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9122 ; 0.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 634 ; 6.289 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 240 ;30.600 ;24.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1064 ;16.606 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;21.842 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 790 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5670 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1032 ; 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): 3160 ; 0.954 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1312 ; 0.135 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5116 ; 1.818 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2098 ; 2.285 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1934 ; 4.049 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 335 2 REMARK 3 1 B 1 B 335 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1888 ; 0.04 ; 0.05 REMARK 3 TIGHT POSITIONAL 1 B (A): 1888 ; 0.04 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 2572 ; 0.07 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 2572 ; 0.07 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1888 ; 0.28 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 1888 ; 0.28 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2572 ; 0.33 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 2572 ; 0.33 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 335 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0430 47.8090 9.0710 REMARK 3 T TENSOR REMARK 3 T11: 0.1604 T22: 0.0375 REMARK 3 T33: 0.2292 T12: -0.0151 REMARK 3 T13: 0.0246 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 1.3741 L22: 5.0814 REMARK 3 L33: 1.2902 L12: -0.5699 REMARK 3 L13: -0.3826 L23: 0.4171 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.1528 S13: -0.1943 REMARK 3 S21: 0.2674 S22: -0.0121 S23: -0.1248 REMARK 3 S31: -0.0090 S32: 0.0451 S33: 0.0047 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 335 REMARK 3 ORIGIN FOR THE GROUP (A): 3.3560 22.6360 19.9220 REMARK 3 T TENSOR REMARK 3 T11: 0.2651 T22: 0.0499 REMARK 3 T33: 0.1130 T12: -0.0407 REMARK 3 T13: 0.0507 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.5801 L22: 5.0968 REMARK 3 L33: 0.8552 L12: -0.7324 REMARK 3 L13: -0.2898 L23: 0.3193 REMARK 3 S TENSOR REMARK 3 S11: 0.0543 S12: -0.1253 S13: 0.0121 REMARK 3 S21: 0.1949 S22: -0.0025 S23: -0.2171 REMARK 3 S31: -0.1590 S32: 0.1620 S33: -0.0519 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 ADDED IN THE IN THE REMARK 3 RIDING POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 2YGK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-APR-11. REMARK 100 THE DEPOSITION ID IS D_1290048045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97940 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24087 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 35.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 1.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 4.5, 1 M REMARK 280 LITHIUM CHLORIDE, 5% W/V PEG 6K, 50 MM MANGANESE CHLORIDE 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 40.14000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLU A 11 REMARK 465 SER A 12 REMARK 465 HIS A 13 REMARK 465 ASN A 14 REMARK 465 GLU A 47 REMARK 465 GLN A 48 REMARK 465 SER A 49 REMARK 465 GLU A 50 REMARK 465 ASP A 238 REMARK 465 ILE A 239 REMARK 465 GLU A 240 REMARK 465 LYS A 241 REMARK 465 ILE A 242 REMARK 465 SER A 243 REMARK 465 GLU A 244 REMARK 465 ILE A 245 REMARK 465 SER A 336 REMARK 465 GLN A 337 REMARK 465 PHE A 338 REMARK 465 TYR A 339 REMARK 465 GLU B 11 REMARK 465 SER B 12 REMARK 465 HIS B 13 REMARK 465 ASN B 14 REMARK 465 GLU B 47 REMARK 465 GLN B 48 REMARK 465 SER B 49 REMARK 465 GLU B 50 REMARK 465 ASP B 238 REMARK 465 ILE B 239 REMARK 465 GLU B 240 REMARK 465 LYS B 241 REMARK 465 ILE B 242 REMARK 465 SER B 243 REMARK 465 GLU B 244 REMARK 465 ILE B 245 REMARK 465 SER B 336 REMARK 465 GLN B 337 REMARK 465 PHE B 338 REMARK 465 TYR B 339 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 113 CB GLU A 113 CG 0.117 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 GLU B 77 OE1 - CD - OE2 ANGL. DEV. = -7.9 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 ARG A 3 -61.12 -25.61 REMARK 500 ILE A 31 30.72 -162.73 REMARK 500 ASN A 83 -55.09 -28.35 REMARK 500 LEU A 89 -67.62 -102.96 REMARK 500 ASP A 194 -128.94 38.52 REMARK 500 LYS A 253 40.83 -96.34 REMARK 500 ILE B 31 30.26 -164.03 REMARK 500 ASN B 83 -54.67 -28.99 REMARK 500 LEU B 89 -67.44 -101.84 REMARK 500 ASP B 194 -128.47 37.99 REMARK 500 LYS B 253 41.83 -96.19 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 MN A1336 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 ASP A 133 OD2 79.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B1336 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 58 OD1 REMARK 620 2 ASP B 133 OD2 77.7 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 MN A 1336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1336 DBREF 2YGK A 1 339 UNP Q97WH1 Q97WH1_SULSO 1 339 DBREF 2YGK B 1 339 UNP Q97WH1 Q97WH1_SULSO 1 339 SEQRES 1 A 339 MSE ILE ARG LYS ILE TYR ASP LYS LEU VAL GLU SER HIS SEQRES 2 A 339 ASN GLU ILE LYS ASN GLN ILE TYR ASN ILE ALA ASN TYR SEQRES 3 A 339 LEU LYS GLN GLU ILE GLN ASP LYS VAL ASN GLU TYR TRP SEQRES 4 A 339 ASN GLU TYR VAL ILE ASN HIS GLU GLN SER GLU THR CYS SEQRES 5 A 339 LYS PHE VAL ALA ILE ASP GLY GLY SER PHE GLY ARG PRO SEQRES 6 A 339 MSE ARG ILE GLY ILE VAL TYR ALA VAL GLY ALA GLU SER SEQRES 7 A 339 VAL ILE GLY ASP ASN LYS GLY VAL LYS THR LEU SER GLU SEQRES 8 A 339 ASP GLY GLN ILE GLY ILE PHE LYS PRO GLY ASN ASP ALA SEQRES 9 A 339 GLN GLU ARG ILE SER LEU LEU MSE GLU ALA LEU GLU LEU SEQRES 10 A 339 SER LEU ALA LEU ARG ASP GLY SER LYS GLY ASP TYR ILE SEQRES 11 A 339 LEU MSE ASP GLY SER LEU SER LYS LYS ILE GLY ASN LYS SEQRES 12 A 339 VAL ASP ILE GLN GLN PHE SER ASP GLU GLU LEU LYS LEU SEQRES 13 A 339 ILE ARG ASN VAL ASP LEU ASN GLY ILE ILE SER ILE LYS SEQRES 14 A 339 ASP GLU ARG LYS MSE ARG ASP LEU LEU MSE LEU LEU ASN SEQRES 15 A 339 GLN PHE LEU VAL SER LYS ILE ILE GLU GLU TYR ASP GLY SEQRES 16 A 339 ASN VAL LEU TRP ILE SER LYS VAL SER ARG GLY ARG ASP SEQRES 17 A 339 LEU PHE GLY THR ASP TYR PRO ASP ILE THR VAL LEU GLU SEQRES 18 A 339 LEU PHE THR GLU LYS ARG GLY PHE SER LYS LEU ILE ILE SEQRES 19 A 339 LYS ASN ILE ASP ILE GLU LYS ILE SER GLU ILE PRO GLU SEQRES 20 A 339 ILE GLU VAL LEU ARG LYS MSE GLU TYR THR THR PHE TYR SEQRES 21 A 339 THR ARG LEU ASP ASN GLY LYS ARG VAL ILE ARG VAL ASP SEQRES 22 A 339 ILE VAL GLY ARG VAL ASP GLU LYS ILE VAL LYS GLU ILE SEQRES 23 A 339 MSE ASP ARG LEU SER GLY VAL SER ILE LYS GLY TYR PRO SEQRES 24 A 339 PHE PRO LEU LEU LYS ALA HIS MSE ASP VAL ARG PHE SER SEQRES 25 A 339 ALA MSE ASP ARG GLU LYS ILE ILE LYS LEU VAL GLY SER SEQRES 26 A 339 LYS LEU HIS LYS ASP ILE GLU TRP TRP PRO SER GLN PHE SEQRES 27 A 339 TYR SEQRES 1 B 339 MSE ILE ARG LYS ILE TYR ASP LYS LEU VAL GLU SER HIS SEQRES 2 B 339 ASN GLU ILE LYS ASN GLN ILE TYR ASN ILE ALA ASN TYR SEQRES 3 B 339 LEU LYS GLN GLU ILE GLN ASP LYS VAL ASN GLU TYR TRP SEQRES 4 B 339 ASN GLU TYR VAL ILE ASN HIS GLU GLN SER GLU THR CYS SEQRES 5 B 339 LYS PHE VAL ALA ILE ASP GLY GLY SER PHE GLY ARG PRO SEQRES 6 B 339 MSE ARG ILE GLY ILE VAL TYR ALA VAL GLY ALA GLU SER SEQRES 7 B 339 VAL ILE GLY ASP ASN LYS GLY VAL LYS THR LEU SER GLU SEQRES 8 B 339 ASP GLY GLN ILE GLY ILE PHE LYS PRO GLY ASN ASP ALA SEQRES 9 B 339 GLN GLU ARG ILE SER LEU LEU MSE GLU ALA LEU GLU LEU SEQRES 10 B 339 SER LEU ALA LEU ARG ASP GLY SER LYS GLY ASP TYR ILE SEQRES 11 B 339 LEU MSE ASP GLY SER LEU SER LYS LYS ILE GLY ASN LYS SEQRES 12 B 339 VAL ASP ILE GLN GLN PHE SER ASP GLU GLU LEU LYS LEU SEQRES 13 B 339 ILE ARG ASN VAL ASP LEU ASN GLY ILE ILE SER ILE LYS SEQRES 14 B 339 ASP GLU ARG LYS MSE ARG ASP LEU LEU MSE LEU LEU ASN SEQRES 15 B 339 GLN PHE LEU VAL SER LYS ILE ILE GLU GLU TYR ASP GLY SEQRES 16 B 339 ASN VAL LEU TRP ILE SER LYS VAL SER ARG GLY ARG ASP SEQRES 17 B 339 LEU PHE GLY THR ASP TYR PRO ASP ILE THR VAL LEU GLU SEQRES 18 B 339 LEU PHE THR GLU LYS ARG GLY PHE SER LYS LEU ILE ILE SEQRES 19 B 339 LYS ASN ILE ASP ILE GLU LYS ILE SER GLU ILE PRO GLU SEQRES 20 B 339 ILE GLU VAL LEU ARG LYS MSE GLU TYR THR THR PHE TYR SEQRES 21 B 339 THR ARG LEU ASP ASN GLY LYS ARG VAL ILE ARG VAL ASP SEQRES 22 B 339 ILE VAL GLY ARG VAL ASP GLU LYS ILE VAL LYS GLU ILE SEQRES 23 B 339 MSE ASP ARG LEU SER GLY VAL SER ILE LYS GLY TYR PRO SEQRES 24 B 339 PHE PRO LEU LEU LYS ALA HIS MSE ASP VAL ARG PHE SER SEQRES 25 B 339 ALA MSE ASP ARG GLU LYS ILE ILE LYS LEU VAL GLY SER SEQRES 26 B 339 LYS LEU HIS LYS ASP ILE GLU TRP TRP PRO SER GLN PHE SEQRES 27 B 339 TYR MODRES 2YGK MSE A 1 MET SELENOMETHIONINE MODRES 2YGK MSE A 66 MET SELENOMETHIONINE MODRES 2YGK MSE A 112 MET SELENOMETHIONINE MODRES 2YGK MSE A 132 MET SELENOMETHIONINE MODRES 2YGK MSE A 174 MET SELENOMETHIONINE MODRES 2YGK MSE A 179 MET SELENOMETHIONINE MODRES 2YGK MSE A 254 MET SELENOMETHIONINE MODRES 2YGK MSE A 287 MET SELENOMETHIONINE MODRES 2YGK MSE A 307 MET SELENOMETHIONINE MODRES 2YGK MSE A 314 MET SELENOMETHIONINE MODRES 2YGK MSE B 1 MET SELENOMETHIONINE MODRES 2YGK MSE B 66 MET SELENOMETHIONINE MODRES 2YGK MSE B 112 MET SELENOMETHIONINE MODRES 2YGK MSE B 132 MET SELENOMETHIONINE MODRES 2YGK MSE B 174 MET SELENOMETHIONINE MODRES 2YGK MSE B 179 MET SELENOMETHIONINE MODRES 2YGK MSE B 254 MET SELENOMETHIONINE MODRES 2YGK MSE B 287 MET SELENOMETHIONINE MODRES 2YGK MSE B 307 MET SELENOMETHIONINE MODRES 2YGK MSE B 314 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 66 8 HET MSE A 112 8 HET MSE A 132 8 HET MSE A 174 8 HET MSE A 179 16 HET MSE A 254 8 HET MSE A 287 8 HET MSE A 307 8 HET MSE A 314 8 HET MSE B 1 8 HET MSE B 66 8 HET MSE B 112 8 HET MSE B 132 8 HET MSE B 174 8 HET MSE B 179 16 HET MSE B 254 8 HET MSE B 287 8 HET MSE B 307 8 HET MSE B 314 8 HET MN A1336 1 HET MN B1336 1 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *66(H2 O) HELIX 1 1 ILE A 2 VAL A 10 1 9 HELIX 2 2 ILE A 16 TYR A 38 1 23 HELIX 3 3 ASP A 103 GLY A 124 1 22 HELIX 4 4 SER A 125 GLY A 127 5 3 HELIX 5 5 SER A 135 GLY A 141 1 7 HELIX 6 6 SER A 150 VAL A 160 1 11 HELIX 7 7 ASP A 161 SER A 167 1 7 HELIX 8 8 ASP A 170 ASP A 194 1 25 HELIX 9 9 PRO A 215 THR A 224 1 10 HELIX 10 10 GLU A 247 ARG A 252 5 6 HELIX 11 11 ASP A 279 GLY A 292 1 14 HELIX 12 12 PHE A 300 ARG A 310 1 11 HELIX 13 13 SER A 312 ILE A 331 1 20 HELIX 14 14 ILE B 2 VAL B 10 1 9 HELIX 15 15 ILE B 16 TYR B 38 1 23 HELIX 16 16 ASP B 103 GLY B 124 1 22 HELIX 17 17 SER B 125 GLY B 127 5 3 HELIX 18 18 SER B 135 GLY B 141 1 7 HELIX 19 19 SER B 150 VAL B 160 1 11 HELIX 20 20 ASP B 161 SER B 167 1 7 HELIX 21 21 ASP B 170 ASP B 194 1 25 HELIX 22 22 PRO B 215 THR B 224 1 10 HELIX 23 23 GLU B 247 ARG B 252 5 6 HELIX 24 24 ASP B 279 GLY B 292 1 14 HELIX 25 25 PHE B 300 ARG B 310 1 11 HELIX 26 26 SER B 312 ILE B 331 1 20 SHEET 1 AA 9 TRP A 39 GLU A 41 0 SHEET 2 AA 9 GLY A 228 SER A 230 -1 O PHE A 229 N ASN A 40 SHEET 3 AA 9 GLU A 255 ARG A 262 -1 O TYR A 260 N SER A 230 SHEET 4 AA 9 ILE A 270 VAL A 275 -1 O ILE A 270 N THR A 261 SHEET 5 AA 9 VAL A 197 SER A 201 -1 O TRP A 199 N ASP A 273 SHEET 6 AA 9 TYR A 129 ASP A 133 1 O ILE A 130 N LEU A 198 SHEET 7 AA 9 PHE A 54 PRO A 65 1 O VAL A 55 N LEU A 131 SHEET 8 AA 9 ILE A 70 ASP A 82 -1 O VAL A 71 N ARG A 64 SHEET 9 AA 9 GLY A 85 PHE A 98 -1 O GLY A 85 N ASP A 82 SHEET 1 AB 4 TRP A 39 GLU A 41 0 SHEET 2 AB 4 GLY A 228 SER A 230 -1 O PHE A 229 N ASN A 40 SHEET 3 AB 4 GLU A 255 ARG A 262 -1 O TYR A 260 N SER A 230 SHEET 4 AB 4 ILE A 233 ASN A 236 -1 O ILE A 233 N THR A 258 SHEET 1 AC 2 SER A 294 ILE A 295 0 SHEET 2 AC 2 TYR A 298 PRO A 299 -1 O TYR A 298 N ILE A 295 SHEET 1 BA 9 TRP B 39 GLU B 41 0 SHEET 2 BA 9 GLY B 228 SER B 230 -1 O PHE B 229 N ASN B 40 SHEET 3 BA 9 GLU B 255 ARG B 262 -1 O TYR B 260 N SER B 230 SHEET 4 BA 9 ILE B 270 VAL B 275 -1 O ILE B 270 N THR B 261 SHEET 5 BA 9 VAL B 197 SER B 201 -1 O TRP B 199 N ASP B 273 SHEET 6 BA 9 TYR B 129 ASP B 133 1 O ILE B 130 N LEU B 198 SHEET 7 BA 9 PHE B 54 PRO B 65 1 O VAL B 55 N LEU B 131 SHEET 8 BA 9 ILE B 70 GLY B 81 -1 O VAL B 71 N ARG B 64 SHEET 9 BA 9 VAL B 86 PHE B 98 -1 O LYS B 87 N ILE B 80 SHEET 1 BB 4 TRP B 39 GLU B 41 0 SHEET 2 BB 4 GLY B 228 SER B 230 -1 O PHE B 229 N ASN B 40 SHEET 3 BB 4 GLU B 255 ARG B 262 -1 O TYR B 260 N SER B 230 SHEET 4 BB 4 ILE B 233 ASN B 236 -1 O ILE B 233 N THR B 258 SHEET 1 BC 2 SER B 294 ILE B 295 0 SHEET 2 BC 2 TYR B 298 PRO B 299 -1 O TYR B 298 N ILE B 295 LINK C MSE A 1 N ILE A 2 1555 1555 1.33 LINK C PRO A 65 N MSE A 66 1555 1555 1.31 LINK C MSE A 66 N ARG A 67 1555 1555 1.33 LINK C LEU A 111 N MSE A 112 1555 1555 1.33 LINK C MSE A 112 N GLU A 113 1555 1555 1.33 LINK C LEU A 131 N MSE A 132 1555 1555 1.33 LINK C MSE A 132 N ASP A 133 1555 1555 1.34 LINK C LYS A 173 N MSE A 174 1555 1555 1.33 LINK C MSE A 174 N ARG A 175 1555 1555 1.33 LINK C LEU A 178 N AMSE A 179 1555 1555 1.33 LINK C LEU A 178 N BMSE A 179 1555 1555 1.33 LINK C AMSE A 179 N LEU A 180 1555 1555 1.33 LINK C BMSE A 179 N LEU A 180 1555 1555 1.33 LINK C LYS A 253 N MSE A 254 1555 1555 1.34 LINK C MSE A 254 N GLU A 255 1555 1555 1.33 LINK C ILE A 286 N MSE A 287 1555 1555 1.33 LINK C MSE A 287 N ASP A 288 1555 1555 1.33 LINK C HIS A 306 N MSE A 307 1555 1555 1.32 LINK C MSE A 307 N ASP A 308 1555 1555 1.31 LINK C ALA A 313 N MSE A 314 1555 1555 1.33 LINK C MSE A 314 N ASP A 315 1555 1555 1.34 LINK C MSE B 1 N ILE B 2 1555 1555 1.32 LINK C PRO B 65 N MSE B 66 1555 1555 1.31 LINK C MSE B 66 N ARG B 67 1555 1555 1.33 LINK C LEU B 111 N MSE B 112 1555 1555 1.33 LINK C MSE B 112 N GLU B 113 1555 1555 1.33 LINK C LEU B 131 N MSE B 132 1555 1555 1.32 LINK C MSE B 132 N ASP B 133 1555 1555 1.34 LINK C LYS B 173 N MSE B 174 1555 1555 1.33 LINK C MSE B 174 N ARG B 175 1555 1555 1.33 LINK C LEU B 178 N BMSE B 179 1555 1555 1.33 LINK C LEU B 178 N AMSE B 179 1555 1555 1.33 LINK C BMSE B 179 N LEU B 180 1555 1555 1.34 LINK C AMSE B 179 N LEU B 180 1555 1555 1.34 LINK C LYS B 253 N MSE B 254 1555 1555 1.33 LINK C MSE B 254 N GLU B 255 1555 1555 1.33 LINK C ILE B 286 N MSE B 287 1555 1555 1.33 LINK C MSE B 287 N ASP B 288 1555 1555 1.34 LINK C HIS B 306 N MSE B 307 1555 1555 1.32 LINK C MSE B 307 N ASP B 308 1555 1555 1.32 LINK C ALA B 313 N MSE B 314 1555 1555 1.33 LINK C MSE B 314 N ASP B 315 1555 1555 1.33 LINK OD1 ASP A 58 MN MN A1336 1555 1555 2.40 LINK OD2 ASP A 133 MN MN A1336 1555 1555 2.49 LINK OD1 ASP B 58 MN MN B1336 1555 1555 2.44 LINK OD2 ASP B 133 MN MN B1336 1555 1555 2.48 SITE 1 AC1 2 ASP A 58 ASP A 133 SITE 1 AC2 3 ASP B 58 GLY B 59 ASP B 133 CRYST1 67.740 80.280 67.670 90.00 107.17 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 0.014762 0.000000 0.004561 0.00000 SCALE2 0.000000 0.012456 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015467 0.00000 MTRIX1 1 -0.295200 0.000000 0.955400 0.02526 1 MTRIX2 1 -0.000230 -1.000000 0.000000 70.45000 1 MTRIX3 1 0.955400 -0.000212 0.295200 -0.00220 1 HETATM 1 N MSE A 1 -9.643 30.750 11.404 1.00 78.83 N ANISOU 1 N MSE A 1 5410 5262 19279 -1863 3486 -558 N HETATM 2 CA MSE A 1 -9.806 31.643 12.580 1.00 78.64 C ANISOU 2 CA MSE A 1 5510 5263 19105 -1797 3949 -400 C HETATM 3 C MSE A 1 -11.100 31.243 13.204 1.00 83.12 C ANISOU 3 C MSE A 1 5702 5512 20365 -1929 4424 -415 C HETATM 4 O MSE A 1 -11.910 30.625 12.544 1.00 86.34 O ANISOU 4 O MSE A 1 5688 5737 21379 -2044 4272 -587 O HETATM 5 CB MSE A 1 -9.827 33.087 12.120 1.00 76.94 C ANISOU 5 CB MSE A 1 5237 5277 18717 -1653 3640 -481 C HETATM 6 CG MSE A 1 -10.202 34.113 13.192 1.00 79.04 C ANISOU 6 CG MSE A 1 5552 5548 18931 -1585 4077 -369 C HETATM 7 SE MSE A 1 -10.391 35.941 12.505 1.00 75.74 SE ANISOU 7 SE MSE A 1 4995 5378 18403 -1406 3667 -496 SE HETATM 8 CE MSE A 1 -12.298 35.832 12.115 1.00 77.69 C ANISOU 8 CE MSE A 1 4474 5325 19718 -1506 3711 -712 C