HEADER HYDROLASE 30-SEP-10 3P1H TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS TITLE 2 V23K/I92A AT CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DELETION UNP RESIDUES 126-131; COMPND 5 EC: 3.1.31.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS STAPHYLOCOCCAL NUCLEASE, HYPERSTABLE VARIANT, HYDROLASE, PDTP, KEYWDS 2 PRESSURE SENSITIVITY, CAVITY EXPDTA X-RAY DIFFRACTION AUTHOR I.A.CLARK,J.A.CARO,G.SUE,J.L.SCHLESSMAN,B.GARCIA-MORENO E,A.HEROUX REVDAT 3 06-SEP-23 3P1H 1 REMARK SEQADV LINK REVDAT 2 12-OCT-11 3P1H 1 HETATM REVDAT 1 05-OCT-11 3P1H 0 JRNL AUTH J.A.CARO,I.A.CLARK,G.SUE,J.L.SCHLESSMAN,B.GARCIA-MORENO E JRNL TITL PRESSURE UNFOLDING EFFECTS OF ARTIFICIAL CAVITIES IN JRNL TITL 2 PROTEINS. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13040 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1298 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 864 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.76000 REMARK 3 B22 (A**2) : -1.31000 REMARK 3 B33 (A**2) : 3.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.37000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.096 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1101 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1485 ; 1.499 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 134 ; 6.370 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 49 ;31.724 ;24.898 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 214 ;16.062 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;18.262 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 157 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 807 ; 0.012 ; 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): 651 ; 1.252 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1042 ; 1.946 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 450 ; 3.270 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 441 ; 4.715 ; 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 : 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): 13.4366 -1.4421 2.8126 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.0718 REMARK 3 T33: 0.0814 T12: 0.0085 REMARK 3 T13: 0.0094 T23: 0.0094 REMARK 3 L TENSOR REMARK 3 L11: 1.5736 L22: 3.0370 REMARK 3 L33: 0.1979 L12: -0.8691 REMARK 3 L13: -0.1046 L23: 0.3829 REMARK 3 S TENSOR REMARK 3 S11: -0.0517 S12: -0.0075 S13: -0.1085 REMARK 3 S21: 0.0297 S22: 0.0926 S23: -0.0579 REMARK 3 S31: 0.0833 S32: 0.0424 S33: -0.0409 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 59 REMARK 3 ORIGIN FOR THE GROUP (A): 14.2726 11.0639 17.3611 REMARK 3 T TENSOR REMARK 3 T11: 0.0858 T22: 0.2742 REMARK 3 T33: 0.0135 T12: 0.0308 REMARK 3 T13: -0.0461 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 2.5916 L22: 11.5828 REMARK 3 L33: 4.4043 L12: 2.9790 REMARK 3 L13: 1.4788 L23: 3.6518 REMARK 3 S TENSOR REMARK 3 S11: -0.1796 S12: -0.5207 S13: -0.2242 REMARK 3 S21: 0.1722 S22: 0.1312 S23: -0.6113 REMARK 3 S31: -0.0982 S32: 0.4518 S33: 0.0485 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 60 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 8.0108 -2.5106 5.5564 REMARK 3 T TENSOR REMARK 3 T11: 0.1031 T22: 0.0634 REMARK 3 T33: 0.1113 T12: 0.0073 REMARK 3 T13: 0.0155 T23: 0.0383 REMARK 3 L TENSOR REMARK 3 L11: 1.8617 L22: 2.3573 REMARK 3 L33: 0.6375 L12: -0.0079 REMARK 3 L13: 0.5191 L23: 0.7814 REMARK 3 S TENSOR REMARK 3 S11: -0.0480 S12: -0.0111 S13: -0.3011 REMARK 3 S21: 0.2036 S22: 0.0193 S23: 0.0467 REMARK 3 S31: 0.1670 S32: -0.1011 S33: 0.0287 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 81 A 123 REMARK 3 ORIGIN FOR THE GROUP (A): 7.6176 6.8054 1.7876 REMARK 3 T TENSOR REMARK 3 T11: 0.0588 T22: 0.0751 REMARK 3 T33: 0.0627 T12: -0.0106 REMARK 3 T13: 0.0085 T23: 0.0158 REMARK 3 L TENSOR REMARK 3 L11: 2.0870 L22: 2.2412 REMARK 3 L33: 0.3438 L12: -0.9005 REMARK 3 L13: 0.0438 L23: 0.4473 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: 0.0770 S13: 0.0548 REMARK 3 S21: -0.0698 S22: 0.0629 S23: 0.0361 REMARK 3 S31: 0.0248 S32: 0.0317 S33: -0.0369 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 124 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5383 14.9094 11.1618 REMARK 3 T TENSOR REMARK 3 T11: 0.0691 T22: 0.0473 REMARK 3 T33: 0.0786 T12: 0.0517 REMARK 3 T13: 0.0413 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 10.4388 L22: 2.4456 REMARK 3 L33: 7.8102 L12: -0.3718 REMARK 3 L13: 6.1251 L23: -1.1104 REMARK 3 S TENSOR REMARK 3 S11: -0.0509 S12: -0.1989 S13: 0.2483 REMARK 3 S21: 0.3306 S22: 0.1030 S23: 0.3334 REMARK 3 S31: 0.0504 S32: 0.1477 S33: -0.0521 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 RIDING REMARK 3 POSITIONS; U VALUES: WITH TLS ADDED REMARK 4 REMARK 4 3P1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000061838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : DOUBLE SILLICON (111) CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13067 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.40 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: PDB ID: 3BDC RESIDUES 7-141, DELETED WATERS AND REMARK 200 COFACTORS, ALL B FACTORS SET TO 20.00 A2, TRUNCATED: H8A, T13A, REMARK 200 V23A, Q30A, K64A, T82A, I92A, Y113A, V114A, Y115A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 9.0, 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 30.22400 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 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: 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 TYR A 54 -0.94 66.45 REMARK 500 ASN A 118 51.84 -118.25 REMARK 500 ASN A 138 -103.70 51.24 REMARK 500 ASN A 138 -102.43 51.24 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 151 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 87.4 REMARK 620 3 THR A 41 O 87.9 74.3 REMARK 620 4 GLU A 43 OE2 160.4 111.9 100.0 REMARK 620 5 THP A 150 O4P 97.6 70.8 144.3 86.5 REMARK 620 6 HOH A 171 O 79.9 143.4 138.4 82.4 77.0 REMARK 620 7 HOH A 181 O 82.9 140.2 66.8 83.8 148.7 72.3 REMARK 620 8 HOH A 198 O 131.0 55.4 54.7 66.6 98.1 148.9 105.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 151 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MEH RELATED DB: PDB REMARK 900 STAPHYLOCOCCAL NUCLEASE D+PHS I92A DBREF 3P1H A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 3P1H LYS A 23 UNP P00644 VAL 105 ENGINEERED MUTATION SEQADV 3P1H A UNP P00644 THR 126 DELETION SEQADV 3P1H A UNP P00644 LYS 127 DELETION SEQADV 3P1H A UNP P00644 HIS 128 DELETION SEQADV 3P1H A UNP P00644 PRO 129 DELETION SEQADV 3P1H A UNP P00644 LYS 130 DELETION SEQADV 3P1H A UNP P00644 LYS 131 DELETION SEQADV 3P1H PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 3P1H ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 3P1H ALA A 92 UNP P00644 ILE 174 ENGINEERED MUTATION SEQADV 3P1H GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 3P1H LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 3P1H 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 LYS 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 ALA 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 ASN 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 THP A 150 25 HET CA A 151 1 HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 2 THP C10 H16 N2 O11 P2 FORMUL 3 CA CA 2+ FORMUL 4 HOH *61(H2 O) HELIX 1 1 TYR A 54 ALA A 69 1 16 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 GLU A 135 1 15 HELIX 4 4 LEU A 137 SER A 141 5 5 SHEET 1 A 7 LYS A 97 MET A 98 0 SHEET 2 A 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 A 7 ILE A 72 PHE A 76 -1 N GLU A 73 O TYR A 93 SHEET 4 A 7 LYS A 9 ALA A 17 -1 N GLU A 10 O VAL A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O MET A 26 N THR A 13 SHEET 6 A 7 GLN A 30 LEU A 36 -1 O PHE A 34 N LYS A 23 SHEET 7 A 7 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 1 B 2 VAL A 39 ASP A 40 0 SHEET 2 B 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK OD2 ASP A 21 CA CA A 151 1555 1555 2.84 LINK OD1 ASP A 40 CA CA A 151 1555 1555 2.87 LINK O THR A 41 CA CA A 151 1555 1555 2.92 LINK OE2 GLU A 43 CA CA A 151 1555 1555 3.06 LINK O4P THP A 150 CA CA A 151 1555 1555 3.16 LINK CA CA A 151 O HOH A 171 1555 1555 2.81 LINK CA CA A 151 O HOH A 181 1555 1555 2.83 LINK CA CA A 151 O HOH A 198 1555 1555 2.66 SITE 1 AC1 20 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC1 20 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC1 20 LYS A 127 CA A 151 HOH A 152 HOH A 154 SITE 4 AC1 20 HOH A 160 HOH A 171 HOH A 173 HOH A 177 SITE 5 AC1 20 HOH A 192 HOH A 195 HOH A 202 HOH A 206 SITE 1 AC2 8 ASP A 21 ASP A 40 THR A 41 GLU A 43 SITE 2 AC2 8 THP A 150 HOH A 171 HOH A 181 HOH A 198 CRYST1 31.131 60.448 37.972 90.00 93.56 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 0.032122 0.000000 0.001996 0.00000 SCALE2 0.000000 0.016543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026386 0.00000