PDB Short entry for 4JZV HEADER HYDROLASE/RNA 03-APR-13 4JZV TITLE CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS PYROPHOSPHOHYDROLASE BSRPPH TITLE 2 BOUND TO A NON-HYDROLYSABLE TRIPHOSPHORYLATED DINUCLEOTIDE RNA (PCP- TITLE 3 PGPG) - SECOND GUANOSINE RESIDUE IN GUANOSINE BINDING POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 8-OXO-DGTPASE, 7,8-DIHYDRO-8-OXOGUANINE-TRIPHOSPHATASE, DGTP COMPND 5 PYROPHOSPHOHYDROLASE; COMPND 6 EC: 3.6.1.55; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'-R(*(GCP)P*G)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: BSU30630, MUTTA, YTKD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS NUDIX HYDROLASE, RNA PYROPHOSPHOHYDROLASE, RPPH, CYTOSOL, HYDROLASE- KEYWDS 2 RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.PITON,V.LARUE,Y.THILLIER,A.DORLEANS,O.PELLEGRINI,I.LI DE LA SIERRA- AUTHOR 2 GALLAY,J.J.VASSEUR,F.DEBART,C.TISNE,C.CONDON REVDAT 4 03-APR-24 4JZV 1 REMARK REVDAT 3 28-FEB-24 4JZV 1 REMARK LINK REVDAT 2 10-JUL-13 4JZV 1 JRNL REVDAT 1 08-MAY-13 4JZV 0 JRNL AUTH J.PITON,V.LARUE,Y.THILLIER,A.DORLEANS,O.PELLEGRINI, JRNL AUTH 2 I.LI DE LA SIERRA-GALLAY,J.J.VASSEUR,F.DEBART,C.TISNE, JRNL AUTH 3 C.CONDON JRNL TITL BACILLUS SUBTILIS RNA DEPROTECTION ENZYME RPPH RECOGNIZES JRNL TITL 2 GUANOSINE IN THE SECOND POSITION OF ITS SUBSTRATES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 8858 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23610407 JRNL DOI 10.1073/PNAS.1221510110 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER-TNT BUSTER 2.10.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 16024 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.150 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.35 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.24 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2760 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2500 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2613 REMARK 3 BIN R VALUE (WORKING SET) : 0.2497 REMARK 3 BIN FREE R VALUE : 0.2566 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.33 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2558 REMARK 3 NUCLEIC ACID ATOMS : 37 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.39360 REMARK 3 B22 (A**2) : 3.95110 REMARK 3 B33 (A**2) : -0.55760 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.380 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.349 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2675 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3600 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 965 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 69 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 364 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2675 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 316 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2789 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.94 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 1.91 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.60 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): -12.3902 18.0495 -10.0626 REMARK 3 T TENSOR REMARK 3 T11: -0.1064 T22: -0.1165 REMARK 3 T33: -0.1053 T12: -0.0424 REMARK 3 T13: 0.0014 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 2.5899 L22: 7.8072 REMARK 3 L33: 2.5340 L12: 1.2353 REMARK 3 L13: 0.5096 L23: 1.1344 REMARK 3 S TENSOR REMARK 3 S11: -0.0408 S12: 0.0559 S13: -0.1182 REMARK 3 S21: 0.1254 S22: -0.0699 S23: 0.1445 REMARK 3 S31: 0.4097 S32: -0.0204 S33: 0.1106 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 17.4654 17.3438 6.7226 REMARK 3 T TENSOR REMARK 3 T11: -0.0908 T22: -0.1174 REMARK 3 T33: -0.1799 T12: -0.0372 REMARK 3 T13: -0.0407 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 2.7346 L22: 11.5019 REMARK 3 L33: 3.6874 L12: -0.3533 REMARK 3 L13: -0.0551 L23: -1.7965 REMARK 3 S TENSOR REMARK 3 S11: 0.0850 S12: 0.0157 S13: -0.0843 REMARK 3 S21: -0.6907 S22: 0.0566 S23: 0.4986 REMARK 3 S31: 0.5442 S32: -0.2718 S33: -0.1416 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JZV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000078713. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9720 REMARK 200 MONOCHROMATOR : DIAMOND (1 1 1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16071 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 69.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.64000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: STRUCTURE OF BSRPPH E68A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES PH 7.5, 25% PEG 1000, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.07900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 69.01250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.07900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 69.01250 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 LYS B 91 REMARK 465 GLU B 92 REMARK 465 LYS B 93 REMARK 465 ASP B 112 REMARK 465 TYR B 113 REMARK 465 GLU B 158 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 GLN A 19 64.44 38.81 REMARK 500 PHE A 114 -119.16 60.03 REMARK 500 ASP B 6 -169.13 -77.28 REMARK 500 GLN B 19 71.24 41.09 REMARK 500 ARG B 131 41.90 -107.88 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 52 O REMARK 620 2 GLU A 72 OE2 81.5 REMARK 620 3 HOH A 329 O 63.1 68.5 REMARK 620 4 HOH A 330 O 126.8 82.8 63.8 REMARK 620 5 GCP C 1 O3G 115.7 109.5 177.7 117.5 REMARK 620 6 GCP C 1 O2B 113.8 162.5 109.6 81.0 72.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 68 OE2 REMARK 620 2 GLU A 72 OE2 85.6 REMARK 620 3 GLU A 115 OE1 166.0 84.5 REMARK 620 4 HOH A 332 O 114.3 121.9 79.4 REMARK 620 5 GCP C 1 O3G 82.1 92.9 88.6 141.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 68 OE2 REMARK 620 2 GLU B 72 OE2 83.2 REMARK 620 3 GLU B 115 OE2 154.3 84.5 REMARK 620 4 HOH B 307 O 131.4 114.8 74.2 REMARK 620 5 HOH B 337 O 117.4 58.2 73.8 56.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JZS RELATED DB: PDB REMARK 900 RELATED ID: 4JZT RELATED DB: PDB REMARK 900 RELATED ID: 4JZU RELATED DB: PDB REMARK 900 RELATED ID: 4JZV RELATED DB: PDB DBREF 4JZV A 1 158 UNP O35013 YTKD_BACSU 1 158 DBREF 4JZV B 1 158 UNP O35013 YTKD_BACSU 1 158 DBREF 4JZV C 1 2 PDB 4JZV 4JZV 1 2 SEQRES 1 A 158 MET TYR GLU PHE LYS ASP TYR TYR GLN ASN THR VAL GLN SEQRES 2 A 158 LEU SER PHE ASP ASP GLN PRO PHE SER ASP SER PRO LYS SEQRES 3 A 158 HIS VAL TRP VAL ILE CYS ARG PHE GLY GLY LYS TRP LEU SEQRES 4 A 158 LEU THR GLU HIS GLU ASP ARG GLY TYR GLU PHE PRO GLY SEQRES 5 A 158 GLY LYS VAL GLU PRO MET GLU CYS ALA GLU GLU ALA ALA SEQRES 6 A 158 LEU ARG GLU VAL LYS GLU GLU THR GLY ALA ARG VAL LYS SEQRES 7 A 158 SER LEU LYS TYR LEU GLY GLN TYR LYS VAL LEU GLY LYS SEQRES 8 A 158 GLU LYS VAL ILE VAL LYS ASN ILE TYR PHE ALA ASP ILE SEQRES 9 A 158 GLU LYS LEU GLU LYS GLN ALA ASP TYR PHE GLU THR LYS SEQRES 10 A 158 GLY PRO VAL LEU PHE HIS GLU LEU PRO GLU ASN LEU SER SEQRES 11 A 158 ARG ASN LYS LYS PHE SER PHE ILE MET LYS ASP SER VAL SEQRES 12 A 158 LEU PRO ILE SER LEU LYS LYS LEU LYS GLU SER GLY TRP SEQRES 13 A 158 ILE GLU SEQRES 1 B 158 MET TYR GLU PHE LYS ASP TYR TYR GLN ASN THR VAL GLN SEQRES 2 B 158 LEU SER PHE ASP ASP GLN PRO PHE SER ASP SER PRO LYS SEQRES 3 B 158 HIS VAL TRP VAL ILE CYS ARG PHE GLY GLY LYS TRP LEU SEQRES 4 B 158 LEU THR GLU HIS GLU ASP ARG GLY TYR GLU PHE PRO GLY SEQRES 5 B 158 GLY LYS VAL GLU PRO MET GLU CYS ALA GLU GLU ALA ALA SEQRES 6 B 158 LEU ARG GLU VAL LYS GLU GLU THR GLY ALA ARG VAL LYS SEQRES 7 B 158 SER LEU LYS TYR LEU GLY GLN TYR LYS VAL LEU GLY LYS SEQRES 8 B 158 GLU LYS VAL ILE VAL LYS ASN ILE TYR PHE ALA ASP ILE SEQRES 9 B 158 GLU LYS LEU GLU LYS GLN ALA ASP TYR PHE GLU THR LYS SEQRES 10 B 158 GLY PRO VAL LEU PHE HIS GLU LEU PRO GLU ASN LEU SER SEQRES 11 B 158 ARG ASN LYS LYS PHE SER PHE ILE MET LYS ASP SER VAL SEQRES 12 B 158 LEU PRO ILE SER LEU LYS LYS LEU LYS GLU SER GLY TRP SEQRES 13 B 158 ILE GLU SEQRES 1 C 2 GCP G HET GCP C 1 14 HET MG A 201 1 HET MG A 202 1 HET EPE A 203 15 HET MG B 201 1 HETNAM GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 GCP C11 H18 N5 O13 P3 FORMUL 4 MG 3(MG 2+) FORMUL 6 EPE C8 H18 N2 O4 S FORMUL 8 HOH *70(H2 O) HELIX 1 1 CYS A 60 GLY A 74 1 15 HELIX 2 2 ASN A 128 ASN A 132 5 5 HELIX 3 3 SER A 136 LYS A 140 5 5 HELIX 4 4 SER A 142 SER A 154 1 13 HELIX 5 5 CYS B 60 GLY B 74 1 15 HELIX 6 6 SER B 136 LYS B 140 5 5 HELIX 7 7 SER B 142 GLY B 155 1 14 SHEET 1 A 7 TYR A 2 LYS A 5 0 SHEET 2 A 7 THR A 11 SER A 15 -1 O LEU A 14 N TYR A 2 SHEET 3 A 7 ALA A 75 LEU A 89 -1 O LEU A 89 N THR A 11 SHEET 4 A 7 VAL A 94 LEU A 107 -1 O LYS A 97 N TYR A 86 SHEET 5 A 7 HIS A 27 PHE A 34 1 N ARG A 33 O ILE A 104 SHEET 6 A 7 LYS A 37 HIS A 43 -1 O LYS A 37 N PHE A 34 SHEET 7 A 7 GLY A 52 LYS A 54 0 SHEET 1 B 4 GLY A 47 GLU A 49 0 SHEET 2 B 4 LYS A 37 HIS A 43 -1 N THR A 41 O GLU A 49 SHEET 3 B 4 HIS A 27 PHE A 34 -1 N PHE A 34 O LYS A 37 SHEET 4 B 4 THR A 116 PHE A 122 0 SHEET 1 C 7 TYR B 2 LYS B 5 0 SHEET 2 C 7 THR B 11 SER B 15 -1 O LEU B 14 N TYR B 2 SHEET 3 C 7 ALA B 75 VAL B 88 -1 O GLN B 85 N SER B 15 SHEET 4 C 7 ILE B 95 LEU B 107 -1 O LYS B 97 N TYR B 86 SHEET 5 C 7 HIS B 27 PHE B 34 1 N ARG B 33 O ILE B 104 SHEET 6 C 7 LYS B 37 HIS B 43 -1 O LYS B 37 N PHE B 34 SHEET 7 C 7 GLY B 52 LYS B 54 0 SHEET 1 D 4 GLY B 47 GLU B 49 0 SHEET 2 D 4 LYS B 37 HIS B 43 -1 N HIS B 43 O GLY B 47 SHEET 3 D 4 HIS B 27 PHE B 34 -1 N PHE B 34 O LYS B 37 SHEET 4 D 4 THR B 116 PHE B 122 0 LINK O3' GCP C 1 P G C 2 1555 1555 1.60 LINK O GLY A 52 MG MG A 201 1555 1555 2.27 LINK OE2 GLU A 68 MG MG A 202 1555 1555 2.14 LINK OE2 GLU A 72 MG MG A 201 1555 1555 2.30 LINK OE2 GLU A 72 MG MG A 202 1555 1555 2.40 LINK OE1 GLU A 115 MG MG A 202 1555 1555 2.00 LINK MG MG A 201 O HOH A 329 1555 1555 2.83 LINK MG MG A 201 O HOH A 330 1555 1555 2.12 LINK MG MG A 201 O3G GCP C 1 1555 1555 1.97 LINK MG MG A 201 O2B GCP C 1 1555 1555 2.86 LINK MG MG A 202 O HOH A 332 1555 1555 2.25 LINK MG MG A 202 O3G GCP C 1 1555 1555 2.42 LINK OE2 GLU B 68 MG MG B 201 1555 1555 1.96 LINK OE2 GLU B 72 MG MG B 201 1555 1555 2.54 LINK OE2 GLU B 115 MG MG B 201 1555 1555 2.29 LINK MG MG B 201 O HOH B 307 1555 1555 2.75 LINK MG MG B 201 O HOH B 337 1555 1555 2.96 CISPEP 1 GLU A 127 ASN A 128 0 -1.01 SITE 1 AC1 9 GLY A 52 GLY A 53 GLU A 68 GLU A 72 SITE 2 AC1 9 GLU A 115 MG A 202 HOH A 329 HOH A 330 SITE 3 AC1 9 GCP C 1 SITE 1 AC2 6 GLU A 68 GLU A 72 GLU A 115 MG A 201 SITE 2 AC2 6 HOH A 332 GCP C 1 SITE 1 AC3 10 LYS A 37 TYR A 48 LEU A 121 PHE A 122 SITE 2 AC3 10 HIS A 123 HOH A 319 GLU B 42 TYR B 48 SITE 3 AC3 10 LEU B 121 PHE B 122 SITE 1 AC4 6 GLY B 52 GLU B 68 GLU B 72 GLU B 115 SITE 2 AC4 6 HOH B 307 HOH B 337 CRYST1 62.158 138.025 35.684 90.00 90.00 90.00 P 21 21 2 8 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 0.016088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028024 0.00000