HEADER UNKNOWN FUNCTION 18-JUN-20 7CD4 TITLE CRYSTAL STRUCTURE OF THE S103F MUTANT OF BACILLUS SUBTILIS (NATTO) TITLE 2 YABJ PROTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: YABJ PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. NATTO (STRAIN SOURCE 3 BEST195); SOURCE 4 ORGANISM_TAXID: 645657; SOURCE 5 STRAIN: BEST195; SOURCE 6 GENE: YABJ, BSNT_00084; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS MUTANT, HOMOTETRAMER, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR Z.FUJIMOTO,N.KISHINE,K.KIMURA REVDAT 2 29-NOV-23 7CD4 1 REMARK REVDAT 1 03-MAR-21 7CD4 0 JRNL AUTH Z.FUJIMOTO,L.T.T.HONG,N.KISHINE,N.SUZUKI,K.KIMURA JRNL TITL TETRAMER FORMATION OF BACILLUS SUBTILIS YABJ PROTEIN THAT JRNL TITL 2 BELONGS TO YJGF/YER057C/UK114 FAMILY. JRNL REF BIOSCI.BIOTECHNOL.BIOCHEM. V. 85 297 2021 JRNL REFN ISSN 0916-8451 JRNL PMID 33590041 JRNL DOI 10.1093/BBB/ZBAA037 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 32822 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2331 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 133 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3573 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 192 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.41000 REMARK 3 B22 (A**2) : 1.58000 REMARK 3 B33 (A**2) : -1.99000 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): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.593 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3658 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3393 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4964 ; 1.427 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7896 ; 0.927 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 457 ; 5.813 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;35.873 ;25.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 611 ;13.402 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;24.880 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4071 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 689 ; 0.001 ; 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): 1840 ; 2.167 ; 3.321 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1839 ; 2.166 ; 3.320 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2293 ; 3.491 ; 4.963 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2294 ; 3.491 ; 4.964 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1818 ; 2.601 ; 3.666 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1818 ; 2.598 ; 3.666 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2671 ; 4.253 ; 5.363 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3977 ; 6.024 ;39.993 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3971 ; 6.020 ;39.967 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 : NULL 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 7CD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017411. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 0.68400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5Y6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13.5 % PEG 3350, 1 MM ZINC ACETATE, REMARK 280 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS BUFFER PH 5.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 32.05050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.26850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.75300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.26850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.05050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.75300 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -235.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 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 MET A 1 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ALA B 4 REMARK 465 VAL B 5 REMARK 465 HIS B 6 REMARK 465 THR B 7 REMARK 465 LYS B 8 REMARK 465 HIS B 9 REMARK 465 ALA B 10 REMARK 465 PRO B 11 REMARK 465 ALA B 12 REMARK 465 ALA B 13 REMARK 465 ILE B 14 REMARK 465 GLY B 15 REMARK 465 PRO B 16 REMARK 465 TYR B 17 REMARK 465 MET C 1 REMARK 465 THR C 2 REMARK 465 LYS C 3 REMARK 465 ALA C 4 REMARK 465 MET D 1 REMARK 465 THR D 2 REMARK 465 LYS D 3 REMARK 465 ALA D 4 REMARK 465 VAL D 5 REMARK 465 HIS D 6 REMARK 465 THR D 7 REMARK 465 LYS D 8 REMARK 465 HIS D 9 REMARK 465 ALA D 10 REMARK 465 PRO D 11 REMARK 465 ALA D 12 REMARK 465 ALA D 13 REMARK 465 ILE D 14 REMARK 465 GLY D 15 REMARK 465 PRO D 16 REMARK 465 TYR D 17 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 -65.47 -96.23 REMARK 500 PRO A 34 42.33 -75.59 REMARK 500 PHE A 95 73.11 -105.30 REMARK 500 ASP A 96 -70.24 -94.43 REMARK 500 ASP A 113 -9.93 71.50 REMARK 500 PHE B 95 56.42 -96.78 REMARK 500 ASP B 113 -8.97 72.89 REMARK 500 ASN C 24 -116.41 54.53 REMARK 500 PHE C 95 75.94 -102.17 REMARK 500 ASP C 96 -77.47 -97.46 REMARK 500 GLN D 19 -75.09 -70.97 REMARK 500 PRO D 34 43.13 -79.93 REMARK 500 ASP D 96 -82.51 -101.96 REMARK 500 LYS D 112 125.89 -37.29 REMARK 500 ASP D 113 -9.17 68.67 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 6 NE2 REMARK 620 2 HIS A 9 NE2 121.6 REMARK 620 3 GLU A 48 OE1 114.5 99.6 REMARK 620 4 HIS B 98 NE2 78.9 97.8 44.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 307 O REMARK 620 2 HOH A 308 O 91.6 REMARK 620 3 GLU C 119 OE2 164.5 81.1 REMARK 620 4 HOH C 311 O 90.3 90.8 76.3 REMARK 620 5 HOH C 326 O 105.8 88.0 87.7 163.9 REMARK 620 6 HOH C 337 O 89.0 175.2 97.2 84.4 96.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 359 O REMARK 620 2 ASP B 96 OD1 171.6 REMARK 620 3 HOH B 307 O 86.4 100.3 REMARK 620 4 HOH B 308 O 84.2 90.3 92.1 REMARK 620 5 HOH B 310 O 90.4 94.6 91.4 173.4 REMARK 620 6 HOH B 324 O 91.1 82.6 175.3 91.6 84.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 40 OE2 REMARK 620 2 HIS C 6 NE2 77.0 REMARK 620 3 HIS C 9 NE2 73.9 3.2 REMARK 620 4 GLU C 48 OE1 74.8 2.7 2.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 320 O REMARK 620 2 HOH B 331 O 77.3 REMARK 620 3 GLU D 119 OE2 78.9 156.0 REMARK 620 4 HOH D 319 O 79.8 91.4 81.5 REMARK 620 5 HOH D 324 O 93.4 90.8 93.5 172.2 REMARK 620 6 HOH D 327 O 168.7 93.8 109.4 93.6 93.7 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 ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5Y6U RELATED DB: PDB REMARK 900 WILD-TYPE PROTEIN REMARK 900 RELATED ID: 7CD2 RELATED DB: PDB REMARK 900 THE SAME MUTANT PROTEIN FROM A DIFFERENT CRYSTALLIZATION CONDITION. REMARK 900 RELATED ID: 7CD3 RELATED DB: PDB REMARK 900 THE SAME MUTANT PROTEIN FROM A DIFFERENT CRYSTALLIZATION CONDITION. DBREF 7CD4 A 1 125 UNP D4G3D4 D4G3D4_BACNB 1 125 DBREF 7CD4 B 1 125 UNP D4G3D4 D4G3D4_BACNB 1 125 DBREF 7CD4 C 1 125 UNP D4G3D4 D4G3D4_BACNB 1 125 DBREF 7CD4 D 1 125 UNP D4G3D4 D4G3D4_BACNB 1 125 SEQADV 7CD4 PHE A 103 UNP D4G3D4 SER 103 ENGINEERED MUTATION SEQADV 7CD4 PHE B 103 UNP D4G3D4 SER 103 ENGINEERED MUTATION SEQADV 7CD4 PHE C 103 UNP D4G3D4 SER 103 ENGINEERED MUTATION SEQADV 7CD4 PHE D 103 UNP D4G3D4 SER 103 ENGINEERED MUTATION SEQRES 1 A 125 MET THR LYS ALA VAL HIS THR LYS HIS ALA PRO ALA ALA SEQRES 2 A 125 ILE GLY PRO TYR SER GLN GLY ILE ILE VAL ASN ASN MET SEQRES 3 A 125 PHE TYR SER SER GLY GLN ILE PRO LEU THR PRO SER GLY SEQRES 4 A 125 GLU MET VAL ASN GLY ASP ILE LYS GLU GLN THR HIS GLN SEQRES 5 A 125 VAL PHE SER ASN LEU LYS ALA VAL LEU GLU GLU ALA GLY SEQRES 6 A 125 ALA SER PHE GLU THR VAL VAL LYS ALA THR VAL PHE ILE SEQRES 7 A 125 ALA ASP MET GLU GLN PHE ALA GLU VAL ASN GLU VAL TYR SEQRES 8 A 125 GLY GLN TYR PHE ASP THR HIS LYS PRO ALA ARG PHE CYS SEQRES 9 A 125 VAL GLU VAL ALA ARG LEU PRO LYS ASP ALA LEU VAL GLU SEQRES 10 A 125 ILE GLU VAL ILE ALA LEU VAL LYS SEQRES 1 B 125 MET THR LYS ALA VAL HIS THR LYS HIS ALA PRO ALA ALA SEQRES 2 B 125 ILE GLY PRO TYR SER GLN GLY ILE ILE VAL ASN ASN MET SEQRES 3 B 125 PHE TYR SER SER GLY GLN ILE PRO LEU THR PRO SER GLY SEQRES 4 B 125 GLU MET VAL ASN GLY ASP ILE LYS GLU GLN THR HIS GLN SEQRES 5 B 125 VAL PHE SER ASN LEU LYS ALA VAL LEU GLU GLU ALA GLY SEQRES 6 B 125 ALA SER PHE GLU THR VAL VAL LYS ALA THR VAL PHE ILE SEQRES 7 B 125 ALA ASP MET GLU GLN PHE ALA GLU VAL ASN GLU VAL TYR SEQRES 8 B 125 GLY GLN TYR PHE ASP THR HIS LYS PRO ALA ARG PHE CYS SEQRES 9 B 125 VAL GLU VAL ALA ARG LEU PRO LYS ASP ALA LEU VAL GLU SEQRES 10 B 125 ILE GLU VAL ILE ALA LEU VAL LYS SEQRES 1 C 125 MET THR LYS ALA VAL HIS THR LYS HIS ALA PRO ALA ALA SEQRES 2 C 125 ILE GLY PRO TYR SER GLN GLY ILE ILE VAL ASN ASN MET SEQRES 3 C 125 PHE TYR SER SER GLY GLN ILE PRO LEU THR PRO SER GLY SEQRES 4 C 125 GLU MET VAL ASN GLY ASP ILE LYS GLU GLN THR HIS GLN SEQRES 5 C 125 VAL PHE SER ASN LEU LYS ALA VAL LEU GLU GLU ALA GLY SEQRES 6 C 125 ALA SER PHE GLU THR VAL VAL LYS ALA THR VAL PHE ILE SEQRES 7 C 125 ALA ASP MET GLU GLN PHE ALA GLU VAL ASN GLU VAL TYR SEQRES 8 C 125 GLY GLN TYR PHE ASP THR HIS LYS PRO ALA ARG PHE CYS SEQRES 9 C 125 VAL GLU VAL ALA ARG LEU PRO LYS ASP ALA LEU VAL GLU SEQRES 10 C 125 ILE GLU VAL ILE ALA LEU VAL LYS SEQRES 1 D 125 MET THR LYS ALA VAL HIS THR LYS HIS ALA PRO ALA ALA SEQRES 2 D 125 ILE GLY PRO TYR SER GLN GLY ILE ILE VAL ASN ASN MET SEQRES 3 D 125 PHE TYR SER SER GLY GLN ILE PRO LEU THR PRO SER GLY SEQRES 4 D 125 GLU MET VAL ASN GLY ASP ILE LYS GLU GLN THR HIS GLN SEQRES 5 D 125 VAL PHE SER ASN LEU LYS ALA VAL LEU GLU GLU ALA GLY SEQRES 6 D 125 ALA SER PHE GLU THR VAL VAL LYS ALA THR VAL PHE ILE SEQRES 7 D 125 ALA ASP MET GLU GLN PHE ALA GLU VAL ASN GLU VAL TYR SEQRES 8 D 125 GLY GLN TYR PHE ASP THR HIS LYS PRO ALA ARG PHE CYS SEQRES 9 D 125 VAL GLU VAL ALA ARG LEU PRO LYS ASP ALA LEU VAL GLU SEQRES 10 D 125 ILE GLU VAL ILE ALA LEU VAL LYS HET ZN A 201 1 HET CL A 202 1 HET CL A 203 1 HET CL A 204 1 HET CL A 205 1 HET BTB A 206 14 HET ZN B 201 1 HET CL B 202 1 HET MG B 203 1 HET CL B 204 1 HET ZN C 201 1 HET CL C 202 1 HET MG C 203 1 HET CL D 201 1 HET CL D 202 1 HET CL D 203 1 HET MG D 204 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETNAM MG MAGNESIUM ION HETSYN BTB BIS-TRIS BUFFER FORMUL 5 ZN 3(ZN 2+) FORMUL 6 CL 10(CL 1-) FORMUL 10 BTB C8 H19 N O5 FORMUL 13 MG 3(MG 2+) FORMUL 22 HOH *192(H2 O) HELIX 1 AA1 ASP A 45 ALA A 64 1 20 HELIX 2 AA2 SER A 67 GLU A 69 5 3 HELIX 3 AA3 ASP A 80 GLU A 82 5 3 HELIX 4 AA4 GLN A 83 PHE A 95 1 13 HELIX 5 AA5 ASP B 45 ALA B 64 1 20 HELIX 6 AA6 SER B 67 GLU B 69 5 3 HELIX 7 AA7 ASP B 80 GLU B 82 5 3 HELIX 8 AA8 GLN B 83 PHE B 95 1 13 HELIX 9 AA9 ASP C 45 ALA C 64 1 20 HELIX 10 AB1 SER C 67 GLU C 69 5 3 HELIX 11 AB2 ASP C 80 GLU C 82 5 3 HELIX 12 AB3 GLN C 83 PHE C 95 1 13 HELIX 13 AB4 ASP D 45 GLY D 65 1 21 HELIX 14 AB5 SER D 67 GLU D 69 5 3 HELIX 15 AB6 ASP D 80 GLU D 82 5 3 HELIX 16 AB7 GLN D 83 PHE D 95 1 13 SHEET 1 AA110 GLY A 20 VAL A 23 0 SHEET 2 AA110 MET A 26 SER A 29 -1 O TYR A 28 N ILE A 21 SHEET 3 AA110 VAL A 116 LEU A 123 -1 O ALA A 122 N PHE A 27 SHEET 4 AA110 VAL A 71 ILE A 78 -1 N PHE A 77 O GLU A 117 SHEET 5 AA110 ARG A 102 VAL A 107 1 O CYS A 104 N VAL A 76 SHEET 6 AA110 ARG B 102 VAL B 107 -1 O VAL B 105 N PHE A 103 SHEET 7 AA110 VAL B 71 ILE B 78 1 N VAL B 76 O CYS B 104 SHEET 8 AA110 VAL B 116 LEU B 123 -1 O GLU B 117 N PHE B 77 SHEET 9 AA110 MET B 26 SER B 29 -1 N PHE B 27 O ALA B 122 SHEET 10 AA110 GLY B 20 VAL B 23 -1 N ILE B 21 O TYR B 28 SHEET 1 AA210 ILE C 21 VAL C 23 0 SHEET 2 AA210 MET C 26 TYR C 28 -1 O TYR C 28 N ILE C 21 SHEET 3 AA210 VAL C 116 LEU C 123 -1 O ALA C 122 N PHE C 27 SHEET 4 AA210 VAL C 71 ILE C 78 -1 N PHE C 77 O GLU C 117 SHEET 5 AA210 ARG C 102 VAL C 107 1 O CYS C 104 N VAL C 76 SHEET 6 AA210 ARG D 102 VAL D 107 -1 O PHE D 103 N VAL C 105 SHEET 7 AA210 VAL D 71 ILE D 78 1 N VAL D 76 O CYS D 104 SHEET 8 AA210 VAL D 116 LEU D 123 -1 O GLU D 117 N PHE D 77 SHEET 9 AA210 MET D 26 TYR D 28 -1 N PHE D 27 O ALA D 122 SHEET 10 AA210 ILE D 21 VAL D 23 -1 N ILE D 21 O TYR D 28 SSBOND 1 CYS A 104 CYS B 104 1555 1555 2.07 SSBOND 2 CYS C 104 CYS D 104 1555 1555 2.09 LINK NE2 HIS A 6 ZN ZN A 201 1555 1555 2.01 LINK NE2 HIS A 9 ZN ZN A 201 1555 1555 2.00 LINK OE1 GLU A 48 ZN ZN A 201 1555 1555 1.92 LINK ZN ZN A 201 NE2 HIS B 98 4445 1555 2.13 LINK O HOH A 307 MG MG C 203 1555 1555 2.02 LINK O HOH A 308 MG MG C 203 1555 1555 2.13 LINK O HOH A 359 MG MG B 203 4445 1555 1.94 LINK OE2 GLU B 40 ZN ZN C 201 1555 2555 2.01 LINK OE1 GLU B 48 ZN ZN B 201 1555 1555 2.55 LINK OD1 ASP B 96 MG MG B 203 1555 1555 2.16 LINK MG MG B 203 O HOH B 307 1555 1555 2.01 LINK MG MG B 203 O HOH B 308 1555 1555 2.14 LINK MG MG B 203 O HOH B 310 1555 1555 2.12 LINK MG MG B 203 O HOH B 324 1555 1555 2.13 LINK O HOH B 320 MG MG D 204 1555 1555 2.05 LINK O HOH B 331 MG MG D 204 1555 1555 2.26 LINK NE2 HIS C 6 ZN ZN C 201 1555 1555 2.08 LINK NE2 HIS C 9 ZN ZN C 201 1555 1555 2.02 LINK OE1 GLU C 48 ZN ZN C 201 1555 1555 1.77 LINK OE2 GLU C 119 MG MG C 203 1555 1555 2.28 LINK MG MG C 203 O HOH C 311 1555 1555 1.99 LINK MG MG C 203 O HOH C 326 1555 1555 1.95 LINK MG MG C 203 O HOH C 337 1555 1555 2.20 LINK OE2 GLU D 119 MG MG D 204 1555 1555 2.27 LINK MG MG D 204 O HOH D 319 1555 1555 2.00 LINK MG MG D 204 O HOH D 324 1555 1555 1.82 LINK MG MG D 204 O HOH D 327 1555 1555 2.30 SITE 1 AC1 4 HIS A 6 HIS A 9 GLU A 48 HIS B 98 SITE 1 AC2 2 HIS A 51 GLN A 93 SITE 1 AC3 5 LYS A 73 ARG A 102 LYS D 73 ARG D 102 SITE 2 AC3 5 HOH D 323 SITE 1 AC4 5 HIS A 98 ALA A 101 HOH A 327 ASN D 24 SITE 2 AC4 5 HOH D 304 SITE 1 AC5 3 LYS A 58 TYR A 94 HOH A 373 SITE 1 AC6 7 PHE A 77 GLU A 117 SER C 30 GLY C 31 SITE 2 AC6 7 PHE C 77 GLU C 117 GLU C 119 SITE 1 AC7 1 GLU B 48 SITE 1 AC8 2 HIS B 51 GLN B 93 SITE 1 AC9 6 HOH A 359 ASP B 96 HOH B 307 HOH B 308 SITE 2 AC9 6 HOH B 310 HOH B 324 SITE 1 AD1 5 ASN B 24 HOH B 302 HIS C 98 ALA C 101 SITE 2 AD1 5 HOH C 301 SITE 1 AD2 4 GLU B 40 HIS C 6 HIS C 9 GLU C 48 SITE 1 AD3 2 HIS C 51 GLN C 93 SITE 1 AD4 6 HOH A 307 HOH A 308 GLU C 119 HOH C 311 SITE 2 AD4 6 HOH C 326 HOH C 337 SITE 1 AD5 2 HIS D 51 GLN D 93 SITE 1 AD6 4 ASN A 24 HOH A 314 HIS D 98 ALA D 101 SITE 1 AD7 1 PHE D 68 SITE 1 AD8 6 HOH B 320 HOH B 331 GLU D 119 HOH D 319 SITE 2 AD8 6 HOH D 324 HOH D 327 CRYST1 64.101 85.506 106.537 90.00 90.00 90.00 P 21 21 21 16 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 0.015600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009386 0.00000