HEADER HYDROLASE 13-JUN-16 5KGU TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS N118D TITLE 2 AT CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 83-231; COMPND 5 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE; COMPND 6 EC: 3.1.31.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: NUC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS NUCLEASE, HYPERSTABLE, PDTP, HYDROLASE, IONIZABLE GROUP EXPDTA X-RAY DIFFRACTION AUTHOR L.A.SKERRITT,A.C.ROBINSON,J.L.SCHLESSMAN,B.GARCIA-MORENO E. REVDAT 4 27-SEP-23 5KGU 1 REMARK REVDAT 3 25-DEC-19 5KGU 1 REMARK REVDAT 2 13-SEP-17 5KGU 1 REMARK REVDAT 1 22-JUN-16 5KGU 0 JRNL AUTH L.A.SKERRITT,A.C.ROBINSON,J.L.SCHLESSMAN,B.GARCIA-MORENO E. JRNL TITL CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT JRNL TITL 2 DELTA+PHS N118D AT CRYOGENIC TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 10504 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 590 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL 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) : 604 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1033 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.19000 REMARK 3 B22 (A**2) : -1.22000 REMARK 3 B33 (A**2) : 3.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.164 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1101 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1095 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1488 ; 1.880 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2535 ; 0.894 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 7.067 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;32.979 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 216 ;18.136 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;10.553 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 161 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1207 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 234 ; 0.002 ; 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): 523 ; 1.218 ; 1.550 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 522 ; 1.203 ; 1.548 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 654 ; 1.713 ; 2.316 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 : 5 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 7 A 42 REMARK 3 ORIGIN FOR THE GROUP (A): 42.5682 -1.6591 41.5839 REMARK 3 T TENSOR REMARK 3 T11: 0.0566 T22: 0.0559 REMARK 3 T33: 0.0352 T12: 0.0171 REMARK 3 T13: 0.0113 T23: 0.0015 REMARK 3 L TENSOR REMARK 3 L11: 2.5105 L22: 3.8153 REMARK 3 L33: 0.8902 L12: -0.5229 REMARK 3 L13: -0.3491 L23: 0.8487 REMARK 3 S TENSOR REMARK 3 S11: -0.0420 S12: 0.1119 S13: -0.2036 REMARK 3 S21: -0.0051 S22: 0.0749 S23: -0.0971 REMARK 3 S31: 0.1322 S32: 0.0791 S33: -0.0328 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 : A 43 A 53 REMARK 3 ORIGIN FOR THE GROUP (A): 46.1694 12.5062 55.1616 REMARK 3 T TENSOR REMARK 3 T11: 0.1391 T22: 0.1421 REMARK 3 T33: 0.1093 T12: 0.0039 REMARK 3 T13: -0.0507 T23: -0.0390 REMARK 3 L TENSOR REMARK 3 L11: 4.7583 L22: 8.7025 REMARK 3 L33: 9.5400 L12: 2.5069 REMARK 3 L13: -0.6770 L23: 0.3066 REMARK 3 S TENSOR REMARK 3 S11: 0.1167 S12: -0.5323 S13: 0.1020 REMARK 3 S21: 0.0872 S22: 0.1791 S23: -0.6126 REMARK 3 S31: -0.1388 S32: 0.4204 S33: -0.2958 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 54 A 109 REMARK 3 ORIGIN FOR THE GROUP (A): 37.5660 1.7520 44.1531 REMARK 3 T TENSOR REMARK 3 T11: 0.0632 T22: 0.0573 REMARK 3 T33: 0.0264 T12: 0.0064 REMARK 3 T13: 0.0131 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 3.2807 L22: 2.7877 REMARK 3 L33: 1.0905 L12: 0.0188 REMARK 3 L13: 0.3703 L23: 0.7604 REMARK 3 S TENSOR REMARK 3 S11: -0.0445 S12: -0.0027 S13: -0.1530 REMARK 3 S21: 0.1310 S22: 0.0421 S23: 0.1222 REMARK 3 S31: 0.1554 S32: -0.0693 S33: 0.0024 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 110 A 118 REMARK 3 ORIGIN FOR THE GROUP (A): 38.0757 13.1094 36.2245 REMARK 3 T TENSOR REMARK 3 T11: 0.0834 T22: 0.0999 REMARK 3 T33: 0.1225 T12: -0.0262 REMARK 3 T13: 0.0027 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 8.0238 L22: 5.9718 REMARK 3 L33: 4.3489 L12: -2.5815 REMARK 3 L13: -2.6932 L23: -0.6199 REMARK 3 S TENSOR REMARK 3 S11: 0.0194 S12: 0.7026 S13: 0.1332 REMARK 3 S21: -0.5328 S22: -0.2411 S23: 0.0506 REMARK 3 S31: 0.1490 S32: -0.2537 S33: 0.2217 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 119 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 28.2720 13.4744 46.1152 REMARK 3 T TENSOR REMARK 3 T11: 0.0354 T22: 0.0493 REMARK 3 T33: 0.1957 T12: 0.0225 REMARK 3 T13: 0.0074 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 4.4473 L22: 5.3713 REMARK 3 L33: 6.4331 L12: -1.0826 REMARK 3 L13: 0.4768 L23: 2.6720 REMARK 3 S TENSOR REMARK 3 S11: -0.1463 S12: -0.1163 S13: 0.5284 REMARK 3 S21: 0.0283 S22: -0.0167 S23: 0.5997 REMARK 3 S31: -0.4000 S32: -0.2026 S33: 0.1631 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5KGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222025. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 1.171.36.32 REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 1.171.36.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11109 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.01700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.870 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.7 REMARK 200 STARTING MODEL: PDB ENTRY 3BDC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 30.17650 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 ALA A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 142 REMARK 465 ASP A 143 REMARK 465 ASN A 144 REMARK 465 ALA A 145 REMARK 465 ASP A 146 REMARK 465 SER A 147 REMARK 465 GLY A 148 REMARK 465 GLN A 149 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 105 NE - CZ - NH1 ANGL. DEV. = 3.7 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 ILE A 18 -71.34 -116.35 REMARK 500 ASP A 19 -156.95 -148.46 REMARK 500 TYR A 54 -1.04 75.78 REMARK 500 GLN A 80 124.08 -37.17 REMARK 500 LYS A 116 131.89 -35.20 REMARK 500 ASP A 118 55.07 -112.75 REMARK 500 ASN A 119 24.10 -141.34 REMARK 500 ASN A 138 -104.47 51.58 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 79.7 REMARK 620 3 THR A 41 O 91.0 79.2 REMARK 620 4 GLU A 43 OE2 151.8 125.3 105.5 REMARK 620 5 HOH A 316 O 74.5 131.4 140.5 78.3 REMARK 620 6 HOH A 337 O 81.4 138.8 64.8 85.1 76.7 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 CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue THP A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB DBREF 5KGU A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 5KGU A UNP P00644 THR 126 DELETION SEQADV 5KGU A UNP P00644 LYS 127 DELETION SEQADV 5KGU A UNP P00644 HIS 128 DELETION SEQADV 5KGU A UNP P00644 PRO 129 DELETION SEQADV 5KGU A UNP P00644 LYS 130 DELETION SEQADV 5KGU A UNP P00644 LYS 131 DELETION SEQADV 5KGU PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 5KGU ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 5KGU GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 5KGU ASP A 118 UNP P00644 ASN 200 ENGINEERED MUTATION SEQADV 5KGU LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 5KGU ALA A 128 UNP P00644 SER 210 ENGINEERED MUTATION SEQRES 1 A 143 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 A 143 LEU ILE LYS ALA ILE ASP GLY ASP THR VAL LYS LEU MET SEQRES 3 A 143 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 143 ASP THR PRO GLU PHE ASN GLU LYS TYR GLY PRO GLU ALA SEQRES 5 A 143 SER ALA PHE THR LYS LYS MET VAL GLU ASN ALA LYS LYS SEQRES 6 A 143 ILE GLU VAL GLU PHE ASP LYS GLY GLN ARG THR ASP LYS SEQRES 7 A 143 TYR GLY ARG GLY LEU ALA TYR ILE TYR ALA ASP GLY LYS SEQRES 8 A 143 MET VAL ASN GLU ALA LEU VAL ARG GLN GLY LEU ALA LYS SEQRES 9 A 143 VAL ALA TYR VAL TYR LYS GLY ASP ASN THR HIS GLU GLN SEQRES 10 A 143 LEU LEU ARG LYS ALA GLU ALA GLN ALA LYS LYS GLU LYS SEQRES 11 A 143 LEU ASN ILE TRP SER GLU ASP ASN ALA ASP SER GLY GLN HET CA A 201 1 HET THP A 202 25 HETNAM CA CALCIUM ION HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE FORMUL 2 CA CA 2+ FORMUL 3 THP C10 H16 N2 O11 P2 FORMUL 4 HOH *74(H2 O) HELIX 1 AA1 TYR A 54 ALA A 69 1 16 HELIX 2 AA2 VAL A 99 GLN A 106 1 8 HELIX 3 AA3 HIS A 121 GLU A 135 1 15 HELIX 4 AA4 LEU A 137 SER A 141 5 5 SHEET 1 AA1 7 LYS A 97 MET A 98 0 SHEET 2 AA1 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 AA1 7 ILE A 72 GLU A 75 -1 N GLU A 75 O TYR A 91 SHEET 4 AA1 7 GLU A 10 ALA A 17 -1 N GLU A 10 O VAL A 74 SHEET 5 AA1 7 THR A 22 TYR A 27 -1 O LYS A 24 N LYS A 16 SHEET 6 AA1 7 GLN A 30 LEU A 36 -1 O PHE A 34 N VAL A 23 SHEET 7 AA1 7 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 1 AA2 2 VAL A 39 ASP A 40 0 SHEET 2 AA2 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK OD2 ASP A 21 CA CA A 201 1555 1555 2.88 LINK OD1 ASP A 40 CA CA A 201 1555 1555 2.81 LINK O THR A 41 CA CA A 201 1555 1555 2.81 LINK OE2 GLU A 43 CA CA A 201 1555 1555 2.97 LINK CA CA A 201 O HOH A 316 1555 1555 2.84 LINK CA CA A 201 O HOH A 337 1555 1555 2.91 SITE 1 AC1 7 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC1 7 THP A 202 HOH A 316 HOH A 337 SITE 1 AC2 21 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC2 21 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC2 21 LYS A 127 CA A 201 HOH A 307 HOH A 311 SITE 4 AC2 21 HOH A 316 HOH A 317 HOH A 318 HOH A 323 SITE 5 AC2 21 HOH A 327 HOH A 345 HOH A 357 HOH A 360 SITE 6 AC2 21 HOH A 362 CRYST1 31.178 60.353 38.425 90.00 93.52 90.00 P 1 21 1 2 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 0.032074 0.000000 0.001973 0.00000 SCALE2 0.000000 0.016569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026074 0.00000