HEADER REPLICATION 30-JAN-08 2VN2 TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF DNAD PROTEIN FROM TITLE 2 GEOBACILLUS KAUSTOPHILUS HTA426 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMOSOME REPLICATION INITIATION PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-128; COMPND 5 SYNONYM: DNAD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS HTA426; SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET22B KEYWDS DNAD, DNA REPLICATION, PRIMOSOME, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR C.-Y.HUANG,Y.-W.CHANG,W.-T.CHEN,Y.-J.SUN,C.-D.HSIAO REVDAT 4 08-MAY-24 2VN2 1 REMARK LINK REVDAT 3 29-AUG-12 2VN2 1 JRNL REMARK VERSN FORMUL REVDAT 2 24-FEB-09 2VN2 1 VERSN REVDAT 1 12-AUG-08 2VN2 0 JRNL AUTH C.-Y.HUANG,Y.-W.CHANG,W.-T.CHEN JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF GEOBACILLUS JRNL TITL 2 KAUSTOPHILUS HTA426 DNAD PROTEIN. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 375 220 2008 JRNL REFN ISSN 0006-291X JRNL PMID 18703019 JRNL DOI 10.1016/J.BBRC.2008.07.160 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 281278.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 46920 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 SET) : 0.217 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.700 REMARK 3 FREE R VALUE TEST SET COUNT : 4573 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6917 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 654 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.75000 REMARK 3 B22 (A**2) : 3.95000 REMARK 3 B33 (A**2) : 1.81000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.034 REMARK 3 BOND ANGLES (DEGREES) : 2.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.430 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.450 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.560 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 50.84 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED. RESIDUES GLU85 REMARK 3 TO ASN94 AND GLY121 TO SER128 OF CHAIN A ARE DISORDERED. REMARK 3 RESIDUES GLU85 TO ASN94 AND LEU120 TO SER128 OF CHAIN B ARE REMARK 3 DISORDERED. RESIDUES MET1, GLU85 TO ASN94, AND GLY121 TO SER128 REMARK 3 OF CHAIN C ARE DISORDERED. RESIDUES MET1, GLU85 TO ASN94, AND REMARK 3 GLY121 TO SER128 OF CHAIN D ARE DISORDERED. REMARK 4 REMARK 4 2VN2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1290035153. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794, 0.9795, 0.9643 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE CONTROL SOFTWARE REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46920 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 27.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: F 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z+1/2 REMARK 290 7555 -X,Y+1/2,-Z+1/2 REMARK 290 8555 X,-Y+1/2,-Z+1/2 REMARK 290 9555 X+1/2,Y,Z+1/2 REMARK 290 10555 -X+1/2,-Y,Z+1/2 REMARK 290 11555 -X+1/2,Y,-Z+1/2 REMARK 290 12555 X+1/2,-Y,-Z+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z REMARK 290 14555 -X+1/2,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y+1/2,-Z REMARK 290 16555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.35350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 78.61500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.35350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 78.61500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.35350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.61500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.35350 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 78.61500 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 78.61500 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 78.61500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 78.61500 REMARK 290 SMTRY1 12 1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 78.61500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 62.35350 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 62.35350 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 62.35350 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 58.25700 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 62.35350 REMARK 290 SMTRY3 16 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -128.8 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 BIOMT1 2 -1.000000 0.000000 0.000000 116.51400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 BIOMT1 2 -1.000000 0.000000 0.000000 174.77100 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.61500 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 HIS A 86 REMARK 465 THR A 87 REMARK 465 ASP A 88 REMARK 465 GLU A 89 REMARK 465 GLN A 90 REMARK 465 GLY A 91 REMARK 465 ILE A 92 REMARK 465 ARG A 93 REMARK 465 ASN A 94 REMARK 465 ARG A 122 REMARK 465 GLN A 123 REMARK 465 GLU A 124 REMARK 465 GLU A 125 REMARK 465 GLU A 126 REMARK 465 GLU A 127 REMARK 465 SER A 128 REMARK 465 HIS B 86 REMARK 465 THR B 87 REMARK 465 ASP B 88 REMARK 465 GLU B 89 REMARK 465 GLN B 90 REMARK 465 GLY B 91 REMARK 465 ILE B 92 REMARK 465 ARG B 93 REMARK 465 ASN B 94 REMARK 465 GLY B 121 REMARK 465 ARG B 122 REMARK 465 GLN B 123 REMARK 465 GLU B 124 REMARK 465 GLU B 125 REMARK 465 GLU B 126 REMARK 465 GLU B 127 REMARK 465 SER B 128 REMARK 465 MET C 1 REMARK 465 HIS C 86 REMARK 465 THR C 87 REMARK 465 ASP C 88 REMARK 465 GLU C 89 REMARK 465 GLN C 90 REMARK 465 GLY C 91 REMARK 465 ILE C 92 REMARK 465 ARG C 93 REMARK 465 ASN C 94 REMARK 465 GLY C 121 REMARK 465 ARG C 122 REMARK 465 GLN C 123 REMARK 465 GLU C 124 REMARK 465 GLU C 125 REMARK 465 GLU C 126 REMARK 465 GLU C 127 REMARK 465 SER C 128 REMARK 465 MET D 1 REMARK 465 HIS D 86 REMARK 465 THR D 87 REMARK 465 ASP D 88 REMARK 465 GLU D 89 REMARK 465 GLN D 90 REMARK 465 GLY D 91 REMARK 465 ILE D 92 REMARK 465 ARG D 93 REMARK 465 ASN D 94 REMARK 465 GLY D 121 REMARK 465 ARG D 122 REMARK 465 GLN D 123 REMARK 465 GLU D 124 REMARK 465 GLU D 125 REMARK 465 GLU D 126 REMARK 465 GLU D 127 REMARK 465 SER D 128 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 85 CA C O CB CG CD OE1 REMARK 470 GLU A 85 OE2 REMARK 470 GLY A 121 CA C O REMARK 470 GLU B 85 CA C O CB CG CD OE1 REMARK 470 GLU B 85 OE2 REMARK 470 LEU B 120 CA C O CB CG CD1 CD2 REMARK 470 GLU C 85 CA C O CB CG CD OE1 REMARK 470 GLU C 85 OE2 REMARK 470 LEU C 120 CA C O CB CG CD1 CD2 REMARK 470 GLU D 85 CA C O CB CG CD OE1 REMARK 470 GLU D 85 OE2 REMARK 470 LEU D 120 CA C O CB CG CD1 CD2 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 O HOH A 2019 O HOH A 2020 1.39 REMARK 500 CE1 TYR D 111 O HOH D 2048 1.45 REMARK 500 O HOH A 2025 O HOH C 2011 1.60 REMARK 500 CZ TYR D 111 O HOH D 2048 1.61 REMARK 500 OH TYR D 111 O HOH D 2048 1.78 REMARK 500 O HOH D 2012 O HOH D 2013 1.83 REMARK 500 O HOH D 2014 O HOH D 2026 1.85 REMARK 500 O HOH B 2010 O HOH B 2020 1.86 REMARK 500 O HOH D 2007 O HOH D 2023 1.90 REMARK 500 OE1 GLU C 70 O HOH C 2035 1.94 REMARK 500 O HOH D 2012 O HOH D 2014 1.95 REMARK 500 O HOH D 2025 O HOH D 2046 1.97 REMARK 500 OE1 GLN B 27 NE2 HIS B 109 2.07 REMARK 500 O HOH C 2020 O HOH C 2043 2.11 REMARK 500 O HOH C 2015 O HOH C 2036 2.15 REMARK 500 O HOH A 2004 O HOH A 2005 2.16 REMARK 500 CG GLN A 42 O HOH A 2021 2.17 REMARK 500 OE2 GLU B 67 O HOH B 2031 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 27 CG GLN A 27 CD 0.147 REMARK 500 VAL A 36 CB VAL A 36 CG1 0.140 REMARK 500 GLU A 59 CG GLU A 59 CD 0.128 REMARK 500 VAL A 72 CB VAL A 72 CG2 0.176 REMARK 500 ARG A 74 CG ARG A 74 CD 0.155 REMARK 500 TRP A 103 CE3 TRP A 103 CZ3 0.114 REMARK 500 GLN B 27 CG GLN B 27 CD 0.156 REMARK 500 GLU B 46 CD GLU B 46 OE2 0.067 REMARK 500 ARG B 74 CG ARG B 74 CD 0.173 REMARK 500 GLU B 100 CG GLU B 100 CD 0.107 REMARK 500 TYR B 111 CD1 TYR B 111 CE1 0.098 REMARK 500 TYR B 111 CZ TYR B 111 CE2 0.125 REMARK 500 TYR B 111 CE2 TYR B 111 CD2 0.136 REMARK 500 SER C 43 CB SER C 43 OG -0.086 REMARK 500 GLU C 67 CB GLU C 67 CG -0.127 REMARK 500 GLU C 67 CD GLU C 67 OE1 0.072 REMARK 500 TYR C 111 CG TYR C 111 CD1 0.087 REMARK 500 TYR C 111 CD1 TYR C 111 CE1 0.098 REMARK 500 TYR C 111 CZ TYR C 111 CE2 0.087 REMARK 500 TYR C 111 CE2 TYR C 111 CD2 0.093 REMARK 500 SER D 14 CB SER D 14 OG -0.104 REMARK 500 VAL D 63 CB VAL D 63 CG1 0.128 REMARK 500 GLU D 67 CD GLU D 67 OE1 0.077 REMARK 500 MET D 69 CG MET D 69 SD 0.163 REMARK 500 GLU D 100 CG GLU D 100 CD 0.105 REMARK 500 TYR D 111 CZ TYR D 111 CE2 0.087 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 ILE A 15 CG1 - CB - CG2 ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG A 60 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 60 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 MET A 61 CG - SD - CE ANGL. DEV. = -24.9 DEGREES REMARK 500 MET A 80 CG - SD - CE ANGL. DEV. = -10.4 DEGREES REMARK 500 MET B 80 CG - SD - CE ANGL. DEV. = -10.2 DEGREES REMARK 500 LEU C 10 CA - CB - CG ANGL. DEV. = 16.9 DEGREES REMARK 500 GLU C 67 OE1 - CD - OE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 MET C 80 CG - SD - CE ANGL. DEV. = -13.5 DEGREES REMARK 500 MET D 80 CG - SD - CE ANGL. DEV. = -18.5 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 GLU B 119 48.15 145.10 REMARK 500 GLU C 100 -53.39 -24.31 REMARK 500 GLU C 119 69.17 -171.29 REMARK 500 HIS D 24 -0.54 -144.00 REMARK 500 GLU D 100 -52.58 -28.41 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 C 118 GLU C 119 147.41 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 A1120 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 24 ND1 REMARK 620 2 GLN A 27 OE1 96.7 REMARK 620 3 GLN A 27 NE2 150.3 54.2 REMARK 620 4 HIS A 109 NE2 103.9 125.1 91.0 REMARK 620 5 GLN A 113 OE1 83.0 146.9 124.0 86.6 REMARK 620 6 GLN A 113 NE2 142.7 113.2 65.1 77.5 59.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1120 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 24 NE2 REMARK 620 2 GLN B 27 OE1 88.0 REMARK 620 3 HIS B 109 NE2 99.4 46.0 REMARK 620 4 GLN B 113 OE1 159.9 86.3 90.4 REMARK 620 5 GLN B 113 NE2 106.9 124.9 152.1 61.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1120 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 24 ND1 REMARK 620 2 GLN C 27 NE2 84.8 REMARK 620 3 GLN C 27 OE1 127.1 59.2 REMARK 620 4 HIS C 109 NE2 97.4 96.1 121.9 REMARK 620 5 GLN C 113 OE1 73.5 158.0 132.9 90.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D1120 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 24 ND1 REMARK 620 2 GLN D 27 NE2 89.6 REMARK 620 3 GLN D 27 OE1 150.7 61.3 REMARK 620 4 HIS D 109 NE2 100.2 135.2 98.8 REMARK 620 5 GLN D 113 OE1 78.4 135.6 124.1 89.2 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 1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 1120 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 1120 DBREF 2VN2 A 1 128 UNP Q5KXY1 Q5KXY1_GEOKA 1 128 DBREF 2VN2 B 1 128 UNP Q5KXY1 Q5KXY1_GEOKA 1 128 DBREF 2VN2 C 1 128 UNP Q5KXY1 Q5KXY1_GEOKA 1 128 DBREF 2VN2 D 1 128 UNP Q5KXY1 Q5KXY1_GEOKA 1 128 SEQRES 1 A 128 MET GLU LYS LYS LYS VAL ALA GLU TRP LEU ALA GLN GLY SEQRES 2 A 128 SER ILE ALA VAL PRO LYS LEU LEU LEU GLY HIS TYR LYS SEQRES 3 A 128 GLN LEU GLY LEU GLY GLU GLY GLU LEU VAL LEU LEU LEU SEQRES 4 A 128 HIS MET GLN SER PHE PHE GLU GLU GLY VAL LEU PHE PRO SEQRES 5 A 128 THR PRO ALA GLU LEU ALA GLU ARG MET THR VAL SER ALA SEQRES 6 A 128 ALA GLU CYS MET GLU MET VAL ARG ARG LEU LEU GLN LYS SEQRES 7 A 128 GLY MET ILE ALA ILE GLU GLU HIS THR ASP GLU GLN GLY SEQRES 8 A 128 ILE ARG ASN GLU LYS TYR THR LEU GLU PRO LEU TRP GLU SEQRES 9 A 128 LYS LEU VAL HIS HIS LEU TYR THR GLN ALA ALA GLN GLN SEQRES 10 A 128 GLY GLU LEU GLY ARG GLN GLU GLU GLU GLU SER SEQRES 1 B 128 MET GLU LYS LYS LYS VAL ALA GLU TRP LEU ALA GLN GLY SEQRES 2 B 128 SER ILE ALA VAL PRO LYS LEU LEU LEU GLY HIS TYR LYS SEQRES 3 B 128 GLN LEU GLY LEU GLY GLU GLY GLU LEU VAL LEU LEU LEU SEQRES 4 B 128 HIS MET GLN SER PHE PHE GLU GLU GLY VAL LEU PHE PRO SEQRES 5 B 128 THR PRO ALA GLU LEU ALA GLU ARG MET THR VAL SER ALA SEQRES 6 B 128 ALA GLU CYS MET GLU MET VAL ARG ARG LEU LEU GLN LYS SEQRES 7 B 128 GLY MET ILE ALA ILE GLU GLU HIS THR ASP GLU GLN GLY SEQRES 8 B 128 ILE ARG ASN GLU LYS TYR THR LEU GLU PRO LEU TRP GLU SEQRES 9 B 128 LYS LEU VAL HIS HIS LEU TYR THR GLN ALA ALA GLN GLN SEQRES 10 B 128 GLY GLU LEU GLY ARG GLN GLU GLU GLU GLU SER SEQRES 1 C 128 MET GLU LYS LYS LYS VAL ALA GLU TRP LEU ALA GLN GLY SEQRES 2 C 128 SER ILE ALA VAL PRO LYS LEU LEU LEU GLY HIS TYR LYS SEQRES 3 C 128 GLN LEU GLY LEU GLY GLU GLY GLU LEU VAL LEU LEU LEU SEQRES 4 C 128 HIS MET GLN SER PHE PHE GLU GLU GLY VAL LEU PHE PRO SEQRES 5 C 128 THR PRO ALA GLU LEU ALA GLU ARG MET THR VAL SER ALA SEQRES 6 C 128 ALA GLU CYS MET GLU MET VAL ARG ARG LEU LEU GLN LYS SEQRES 7 C 128 GLY MET ILE ALA ILE GLU GLU HIS THR ASP GLU GLN GLY SEQRES 8 C 128 ILE ARG ASN GLU LYS TYR THR LEU GLU PRO LEU TRP GLU SEQRES 9 C 128 LYS LEU VAL HIS HIS LEU TYR THR GLN ALA ALA GLN GLN SEQRES 10 C 128 GLY GLU LEU GLY ARG GLN GLU GLU GLU GLU SER SEQRES 1 D 128 MET GLU LYS LYS LYS VAL ALA GLU TRP LEU ALA GLN GLY SEQRES 2 D 128 SER ILE ALA VAL PRO LYS LEU LEU LEU GLY HIS TYR LYS SEQRES 3 D 128 GLN LEU GLY LEU GLY GLU GLY GLU LEU VAL LEU LEU LEU SEQRES 4 D 128 HIS MET GLN SER PHE PHE GLU GLU GLY VAL LEU PHE PRO SEQRES 5 D 128 THR PRO ALA GLU LEU ALA GLU ARG MET THR VAL SER ALA SEQRES 6 D 128 ALA GLU CYS MET GLU MET VAL ARG ARG LEU LEU GLN LYS SEQRES 7 D 128 GLY MET ILE ALA ILE GLU GLU HIS THR ASP GLU GLN GLY SEQRES 8 D 128 ILE ARG ASN GLU LYS TYR THR LEU GLU PRO LEU TRP GLU SEQRES 9 D 128 LYS LEU VAL HIS HIS LEU TYR THR GLN ALA ALA GLN GLN SEQRES 10 D 128 GLY GLU LEU GLY ARG GLN GLU GLU GLU GLU SER HET MG A1120 1 HET MG B1120 1 HET MG C1120 1 HET MG D1120 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 4(MG 2+) FORMUL 9 HOH *178(H2 O) HELIX 1 1 GLU A 2 GLN A 12 1 11 HELIX 2 2 LYS A 19 GLY A 23 1 5 HELIX 3 3 GLY A 31 GLU A 46 1 16 HELIX 4 4 THR A 53 ARG A 60 1 8 HELIX 5 5 SER A 64 LYS A 78 1 15 HELIX 6 6 LEU A 99 GLN A 117 1 19 HELIX 7 7 MET B 1 ALA B 11 1 11 HELIX 8 8 LYS B 19 GLY B 23 1 5 HELIX 9 9 GLY B 31 GLU B 47 1 17 HELIX 10 10 THR B 53 GLU B 59 1 7 HELIX 11 11 SER B 64 LYS B 78 1 15 HELIX 12 12 LEU B 99 GLN B 116 1 18 HELIX 13 13 GLU C 2 ALA C 11 1 10 HELIX 14 14 LYS C 19 GLY C 23 1 5 HELIX 15 15 TYR C 25 GLY C 29 5 5 HELIX 16 16 GLY C 31 GLU C 47 1 17 HELIX 17 17 THR C 53 ARG C 60 1 8 HELIX 18 18 SER C 64 LYS C 78 1 15 HELIX 19 19 LEU C 99 GLN C 117 1 19 HELIX 20 20 GLU D 2 ALA D 11 1 10 HELIX 21 21 LYS D 19 GLY D 23 1 5 HELIX 22 22 GLY D 31 GLU D 47 1 17 HELIX 23 23 THR D 53 GLU D 59 1 7 HELIX 24 24 SER D 64 GLY D 79 1 16 HELIX 25 25 LEU D 99 GLN D 117 1 19 SHEET 1 AA 2 SER A 14 PRO A 18 0 SHEET 2 AA 2 SER C 14 PRO C 18 -1 O ILE C 15 N VAL A 17 SHEET 1 AB 2 ALA A 82 ILE A 83 0 SHEET 2 AB 2 TYR A 97 THR A 98 -1 O THR A 98 N ALA A 82 SHEET 1 BA 2 SER B 14 PRO B 18 0 SHEET 2 BA 2 SER D 14 PRO D 18 -1 O ILE D 15 N VAL B 17 SHEET 1 BB 2 ALA B 82 ILE B 83 0 SHEET 2 BB 2 TYR B 97 THR B 98 -1 O THR B 98 N ALA B 82 SHEET 1 CA 2 ALA C 82 ILE C 83 0 SHEET 2 CA 2 TYR C 97 THR C 98 -1 O THR C 98 N ALA C 82 SHEET 1 DA 2 ALA D 82 ILE D 83 0 SHEET 2 DA 2 TYR D 97 THR D 98 -1 O THR D 98 N ALA D 82 LINK ND1 HIS A 24 MG MG A1120 1555 1555 2.30 LINK OE1 GLN A 27 MG MG A1120 1555 1555 2.45 LINK NE2 GLN A 27 MG MG A1120 1555 1555 2.60 LINK NE2 HIS A 109 MG MG A1120 1555 1555 2.24 LINK OE1 GLN A 113 MG MG A1120 1555 1555 2.28 LINK NE2 GLN A 113 MG MG A1120 1555 1555 2.32 LINK NE2 HIS B 24 MG MG B1120 1555 1555 2.62 LINK OE1 GLN B 27 MG MG B1120 1555 1555 2.38 LINK NE2 HIS B 109 MG MG B1120 1555 1555 2.82 LINK OE1 GLN B 113 MG MG B1120 1555 1555 2.28 LINK NE2 GLN B 113 MG MG B1120 1555 1555 2.17 LINK ND1 HIS C 24 MG MG C1120 1555 1555 2.38 LINK NE2 GLN C 27 MG MG C1120 1555 1555 2.31 LINK OE1 GLN C 27 MG MG C1120 1555 1555 2.26 LINK NE2 HIS C 109 MG MG C1120 1555 1555 2.22 LINK OE1 GLN C 113 MG MG C1120 1555 1555 2.29 LINK ND1 HIS D 24 MG MG D1120 1555 1555 2.48 LINK NE2 GLN D 27 MG MG D1120 1555 1555 2.27 LINK OE1 GLN D 27 MG MG D1120 1555 1555 2.14 LINK NE2 HIS D 109 MG MG D1120 1555 1555 2.14 LINK OE1 GLN D 113 MG MG D1120 1555 1555 2.27 SITE 1 AC1 4 HIS A 24 GLN A 27 HIS A 109 GLN A 113 SITE 1 AC2 5 HIS B 24 GLN B 27 HIS B 109 GLN B 113 SITE 2 AC2 5 HOH B2039 SITE 1 AC3 4 HIS C 24 GLN C 27 HIS C 109 GLN C 113 SITE 1 AC4 4 HIS D 24 GLN D 27 HIS D 109 GLN D 113 CRYST1 116.514 124.707 157.230 90.00 90.00 90.00 F 2 2 2 64 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 0.008583 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006360 0.00000