HEADER HYDROLASE 16-JUN-14 4TRD TITLE CRYSTAL STRUCTURE OF STAPHYLCOCCAL NUCLEASE VARIANT DELTA+PHS TITLE 2 I72K/V74K AT PH 9.0 AT CRYOGENIC TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FRAGMENT 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS NUCLEASE, HYPERSTABLE, PDTP, HYDROLASE, IONIZABLE GROUP EXPDTA X-RAY DIFFRACTION AUTHOR J.L.SORENSON,J.L.SCHLESSMAN,E.B.GARCIA-MORENO REVDAT 6 27-SEP-23 4TRD 1 REMARK REVDAT 5 25-DEC-19 4TRD 1 SEQADV REVDAT 4 22-NOV-17 4TRD 1 REMARK REVDAT 3 06-SEP-17 4TRD 1 SOURCE JRNL REMARK REVDAT 2 25-FEB-15 4TRD 1 REMARK REVDAT 1 16-JUL-14 4TRD 0 JRNL AUTH J.L.SORENSON,J.L.SCHLESSMAN,E.B.GARCIA-MORENO JRNL TITL CRYSTAL STRUCTURE OF STAPHYLCOCCAL NUCLEASE VARIANT JRNL TITL 2 DELTA+PHS I72K/V74K AT PH 9.0 AT CRYOGENIC TEMPERATURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 19388 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1053 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.612 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1198 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1191 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1629 ; 1.863 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2779 ; 1.131 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 156 ; 6.879 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;33.975 ;25.714 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 248 ;15.325 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;13.299 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 172 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1350 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 255 ; 0.007 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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): 3.2024 -5.6212 -15.1017 REMARK 3 T TENSOR REMARK 3 T11: 0.0280 T22: 0.0223 REMARK 3 T33: 0.0422 T12: -0.0057 REMARK 3 T13: -0.0042 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.7808 L22: 2.2202 REMARK 3 L33: 0.4420 L12: -0.4717 REMARK 3 L13: -0.0917 L23: -0.0275 REMARK 3 S TENSOR REMARK 3 S11: 0.0008 S12: 0.0187 S13: 0.0572 REMARK 3 S21: 0.0062 S22: 0.0202 S23: 0.0751 REMARK 3 S31: -0.0794 S32: -0.0050 S33: -0.0210 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 69 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9900 -12.9004 -2.9962 REMARK 3 T TENSOR REMARK 3 T11: 0.0469 T22: 0.0353 REMARK 3 T33: 0.0218 T12: 0.0158 REMARK 3 T13: 0.0169 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.7974 L22: 3.8729 REMARK 3 L33: 2.1870 L12: 0.9323 REMARK 3 L13: -0.8370 L23: -1.1303 REMARK 3 S TENSOR REMARK 3 S11: -0.0137 S12: -0.0731 S13: -0.0062 REMARK 3 S21: 0.1807 S22: 0.0470 S23: 0.1368 REMARK 3 S31: 0.0002 S32: -0.1016 S33: -0.0333 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 70 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 10.1413 -4.4969 -19.9504 REMARK 3 T TENSOR REMARK 3 T11: 0.0351 T22: 0.0344 REMARK 3 T33: 0.0568 T12: 0.0031 REMARK 3 T13: 0.0162 T23: 0.0402 REMARK 3 L TENSOR REMARK 3 L11: 4.3511 L22: 6.4473 REMARK 3 L33: 8.6190 L12: 1.1679 REMARK 3 L13: 2.4570 L23: 3.7879 REMARK 3 S TENSOR REMARK 3 S11: -0.0278 S12: 0.0944 S13: 0.1070 REMARK 3 S21: -0.0270 S22: 0.0056 S23: 0.0081 REMARK 3 S31: -0.0326 S32: 0.1651 S33: 0.0222 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 143 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2054 -18.2785 -14.6355 REMARK 3 T TENSOR REMARK 3 T11: 0.0413 T22: 0.0283 REMARK 3 T33: 0.0457 T12: -0.0029 REMARK 3 T13: 0.0079 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.4491 L22: 1.4275 REMARK 3 L33: 1.1422 L12: -0.4242 REMARK 3 L13: 0.4035 L23: -0.0307 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: 0.0262 S13: -0.0966 REMARK 3 S21: -0.0068 S22: 0.0067 S23: 0.0297 REMARK 3 S31: 0.1026 S32: 0.0438 S33: -0.0374 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4TRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000202152. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 9.0 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) : 1.54 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19443 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.49 REMARK 200 R MERGE (I) : 0.02370 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.73 REMARK 200 R MERGE FOR SHELL (I) : 0.18270 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.090 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3BDC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% MPD, 25MM 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 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 15.90450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.91350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.10200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.91350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.90450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.10200 REMARK 290 SMTRY3 4 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 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: 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 OD1 ASN A 51 O HOH A 301 2.15 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 -72.05 -118.60 REMARK 500 ASP A 19 -158.76 -150.28 REMARK 500 TYR A 54 -1.94 77.38 REMARK 500 ASN A 118 53.36 -152.57 REMARK 500 ASN A 138 -109.45 48.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 117 ASN A 118 -144.28 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 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD2 REMARK 620 2 ASP A 40 OD1 85.5 REMARK 620 3 THR A 41 O 88.6 78.4 REMARK 620 4 HOH A 316 O 150.0 105.8 120.6 REMARK 620 5 HOH A 370 O 73.3 136.4 136.6 79.9 REMARK 620 6 HOH A 371 O 80.2 141.0 65.2 104.6 72.9 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 THP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BDC RELATED DB: PDB REMARK 900 RELATED ID: 4PMC RELATED DB: PDB REMARK 900 SAME PROTEIN AT PH 7.0 DBREF 4TRD A 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 4TRD A UNP P00644 THR 126 DELETION SEQADV 4TRD A UNP P00644 LYS 127 DELETION SEQADV 4TRD A UNP P00644 HIS 128 DELETION SEQADV 4TRD A UNP P00644 PRO 129 DELETION SEQADV 4TRD A UNP P00644 LYS 130 DELETION SEQADV 4TRD A UNP P00644 LYS 131 DELETION SEQADV 4TRD PHE A 50 UNP P00644 GLY 132 ENGINEERED MUTATION SEQADV 4TRD ASN A 51 UNP P00644 VAL 133 ENGINEERED MUTATION SEQADV 4TRD LYS A 72 UNP P00644 ILE 154 ENGINEERED MUTATION SEQADV 4TRD LYS A 74 UNP P00644 VAL 156 ENGINEERED MUTATION SEQADV 4TRD GLY A 117 UNP P00644 PRO 199 ENGINEERED MUTATION SEQADV 4TRD LEU A 124 UNP P00644 HIS 206 ENGINEERED MUTATION SEQADV 4TRD 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 LYS GLU LYS 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 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 201 25 HET CA A 202 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 *131(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 6 GLU A 10 PRO A 11 0 SHEET 2 AA1 6 LYS A 72 GLU A 75 -1 O LYS A 74 N GLU A 10 SHEET 3 AA1 6 GLY A 88 ALA A 94 -1 O TYR A 93 N GLU A 73 SHEET 4 AA1 6 GLN A 30 LEU A 36 1 N ARG A 35 O GLY A 88 SHEET 5 AA1 6 THR A 22 TYR A 27 -1 N VAL A 23 O PHE A 34 SHEET 6 AA1 6 LEU A 14 ALA A 17 -1 N LYS A 16 O LYS A 24 SHEET 1 AA2 4 GLU A 10 PRO A 11 0 SHEET 2 AA2 4 LYS A 72 GLU A 75 -1 O LYS A 74 N GLU A 10 SHEET 3 AA2 4 GLY A 88 ALA A 94 -1 O TYR A 93 N GLU A 73 SHEET 4 AA2 4 LYS A 97 MET A 98 -1 O LYS A 97 N ALA A 94 SHEET 1 AA3 2 VAL A 39 ASP A 40 0 SHEET 2 AA3 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 LINK OD2 ASP A 21 CA CA A 202 1555 1555 2.84 LINK OD1 ASP A 40 CA CA A 202 1555 1555 2.70 LINK O THR A 41 CA CA A 202 1555 1555 2.73 LINK CA CA A 202 O HOH A 316 1555 1555 2.89 LINK CA CA A 202 O HOH A 370 1555 1555 2.84 LINK CA CA A 202 O HOH A 371 1555 1555 3.00 SITE 1 AC1 21 ARG A 35 ASP A 40 LYS A 84 TYR A 85 SITE 2 AC1 21 ARG A 87 LEU A 89 TYR A 113 TYR A 115 SITE 3 AC1 21 LYS A 127 CA A 202 HOH A 303 HOH A 304 SITE 4 AC1 21 HOH A 316 HOH A 320 HOH A 331 HOH A 364 SITE 5 AC1 21 HOH A 370 HOH A 373 HOH A 390 HOH A 396 SITE 6 AC1 21 HOH A 426 SITE 1 AC2 7 ASP A 21 ASP A 40 THR A 41 THP A 201 SITE 2 AC2 7 HOH A 316 HOH A 370 HOH A 371 CRYST1 31.809 60.204 73.827 90.00 90.00 90.00 P 21 21 21 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 0.031438 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013545 0.00000