HEADER TRANSFERASE 25-FEB-08 3CC8 TITLE CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (BCE_1332) FROM TITLE 2 BACILLUS CEREUS ATCC 10987 AT 1.64 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 222523; SOURCE 4 STRAIN: ATCC 10987; SOURCE 5 GENE: NP_977653.1, BCE_1332; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PUTATIVE METHYLTRANSFERASE FROM NDP-N-METHYL-L-GLUCOSAMINE KEYWDS 2 BIOSYNTHETIC PATHWAY, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 01-FEB-23 3CC8 1 REMARK SEQADV LINK REVDAT 6 24-JUL-19 3CC8 1 REMARK LINK REVDAT 5 25-OCT-17 3CC8 1 REMARK REVDAT 4 13-JUL-11 3CC8 1 VERSN REVDAT 3 23-MAR-11 3CC8 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 3CC8 1 VERSN REVDAT 1 04-MAR-08 3CC8 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE METHYLTRANSFERASE FROM JRNL TITL 2 NDP-N-METHYL-L-GLUCOSAMINE BIOSYNTHETIC PATHWAY JRNL TITL 3 (NP_977653.1) FROM BACILLUS CEREUS ATCC 10987 AT 1.64 A JRNL TITL 4 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 29307 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1491 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1998 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1664 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 174 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : -0.89000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.814 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1804 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1195 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2462 ; 1.561 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2940 ; 0.981 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 231 ; 6.478 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;35.041 ;24.937 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 312 ;13.441 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;17.299 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 272 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2051 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 363 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 379 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1268 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 899 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 907 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.164 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.149 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.199 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.296 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.087 ; 0.200 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): 1215 ; 2.481 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 449 ; 0.568 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1812 ; 3.039 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 768 ; 5.609 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 650 ; 7.574 ;11.000 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 : 1 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 19 A 229 REMARK 3 ORIGIN FOR THE GROUP (A): 25.5858 33.1978 14.2280 REMARK 3 T TENSOR REMARK 3 T11: -0.0643 T22: -0.0506 REMARK 3 T33: -0.0729 T12: 0.0002 REMARK 3 T13: 0.0244 T23: -0.0075 REMARK 3 L TENSOR REMARK 3 L11: 1.3315 L22: 1.3942 REMARK 3 L33: 1.6335 L12: -0.6809 REMARK 3 L13: 1.3495 L23: -0.6337 REMARK 3 S TENSOR REMARK 3 S11: 0.1014 S12: 0.0947 S13: -0.0553 REMARK 3 S21: -0.0166 S22: -0.0271 S23: 0.0896 REMARK 3 S31: 0.0595 S32: -0.0054 S33: -0.0743 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: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. REMARK 3 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 4. TWO NI ATOMS OF THE A SUBUNIT WERE FOUND IN THE ASYMMETRIC REMARK 3 UNIT. THE FIRST NI ATOM WAS COORDINATED TO THE SIDE CHAIN OF REMARK 3 HIS 188, GLU 192, AND THREE WATERS. THE OTHER NI ATOM WAS REMARK 3 DISORDERED AND DUAL CONFORMATION WERE MODELED. DUAL NI ATOMS REMARK 3 WERE COORDINATED TO THE SIDE CHAINS OF HIS 104, HIS 158, GLU 103 REMARK 3 AND FOUR WATER MOLECULES. ANOMALOUS DIFFERENCE FOURIERS AND REMARK 3 X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF REMARK 3 THE NI IONS. REMARK 4 REMARK 4 3CC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837, 0.97964, 0.97978 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 28.194 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.79200 REMARK 200 R SYM FOR SHELL (I) : 0.79200 REMARK 200 FOR SHELL : 0.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 40.0% MPD, 5.0% PEG 8000, REMARK 280 0.1M CACODYLATE PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 45.61150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.19950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.61150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.19950 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 300 REMARK: AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS REMARK 300 THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.5 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 73.61435 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 49.72528 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 ASN A 2 REMARK 465 SER A 3 REMARK 465 PRO A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 SER A 7 REMARK 465 LEU A 8 REMARK 465 TYR A 9 REMARK 465 GLU A 10 REMARK 465 GLU A 11 REMARK 465 LYS A 12 REMARK 465 SER A 13 REMARK 465 GLY A 14 REMARK 465 HIS A 15 REMARK 465 TYR A 16 REMARK 465 TYR A 17 REMARK 465 ASN A 18 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 LYS A 29 CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 GLU A 67 CD OE1 OE2 REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 LYS A 180 NZ REMARK 470 LYS A 189 CE NZ REMARK 470 GLU A 196 CD OE1 OE2 REMARK 470 LYS A 203 CG CD CE NZ 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 NI NI A 231 O HOH A 365 1.70 REMARK 500 OE1 GLU A 214 OH TYR A 220 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 219 CB GLN A 219 CG -0.167 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 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 41 -135.92 50.16 REMARK 500 PRO A 87 48.39 -85.91 REMARK 500 HIS A 188 19.53 -143.48 REMARK 500 SER A 227 -151.93 -148.31 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 NI A 231 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 103 OE2 REMARK 620 2 HIS A 104 NE2 100.0 REMARK 620 3 HIS A 158 NE2 108.1 92.8 REMARK 620 4 HOH A 365 O 153.5 102.1 85.1 REMARK 620 5 HOH A 382 O 84.6 171.8 92.2 71.8 REMARK 620 6 HOH A 384 O 82.6 84.8 169.3 85.2 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 231 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HOH A 384 O 75.9 REMARK 620 3 HOH A 385 O 105.1 54.6 REMARK 620 4 HOH A 405 O 115.4 151.4 96.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 231 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 383436 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3CC8 A 1 229 UNP Q73BT6 Q73BT6_BACC1 1 229 SEQADV 3CC8 GLY A 0 UNP Q73BT6 EXPRESSION TAG SEQRES 1 A 230 GLY MSE ASN SER PRO LYS ASN SER LEU TYR GLU GLU LYS SEQRES 2 A 230 SER GLY HIS TYR TYR ASN ALA VAL ASN PRO ASN LEU LEU SEQRES 3 A 230 LYS HIS ILE LYS LYS GLU TRP LYS GLU VAL LEU ASP ILE SEQRES 4 A 230 GLY CYS SER SER GLY ALA LEU GLY ALA ALA ILE LYS GLU SEQRES 5 A 230 ASN GLY THR ARG VAL SER GLY ILE GLU ALA PHE PRO GLU SEQRES 6 A 230 ALA ALA GLU GLN ALA LYS GLU LYS LEU ASP HIS VAL VAL SEQRES 7 A 230 LEU GLY ASP ILE GLU THR MSE ASP MSE PRO TYR GLU GLU SEQRES 8 A 230 GLU GLN PHE ASP CYS VAL ILE PHE GLY ASP VAL LEU GLU SEQRES 9 A 230 HIS LEU PHE ASP PRO TRP ALA VAL ILE GLU LYS VAL LYS SEQRES 10 A 230 PRO TYR ILE LYS GLN ASN GLY VAL ILE LEU ALA SER ILE SEQRES 11 A 230 PRO ASN VAL SER HIS ILE SER VAL LEU ALA PRO LEU LEU SEQRES 12 A 230 ALA GLY ASN TRP THR TYR THR GLU TYR GLY LEU LEU ASP SEQRES 13 A 230 LYS THR HIS ILE ARG PHE PHE THR PHE ASN GLU MSE LEU SEQRES 14 A 230 ARG MSE PHE LEU LYS ALA GLY TYR SER ILE SER LYS VAL SEQRES 15 A 230 ASP ARG VAL TYR VAL ASP HIS LYS MSE TYR GLU PRO LEU SEQRES 16 A 230 ILE GLU GLU LEU TYR GLY ILE CYS LYS LYS TYR ARG LEU SEQRES 17 A 230 GLY SER GLY PHE MSE ALA GLU THR VAL VAL PHE GLN TYR SEQRES 18 A 230 ILE ILE GLU ALA GLU LYS SER GLN LEU MODRES 3CC8 MSE A 84 MET SELENOMETHIONINE MODRES 3CC8 MSE A 86 MET SELENOMETHIONINE MODRES 3CC8 MSE A 167 MET SELENOMETHIONINE MODRES 3CC8 MSE A 170 MET SELENOMETHIONINE MODRES 3CC8 MSE A 190 MET SELENOMETHIONINE MODRES 3CC8 MSE A 212 MET SELENOMETHIONINE HET MSE A 84 8 HET MSE A 86 8 HET MSE A 167 8 HET MSE A 170 8 HET MSE A 190 8 HET MSE A 212 8 HET NI A 230 1 HET NI A 231 2 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 NI 2(NI 2+) FORMUL 4 HOH *174(H2 O) HELIX 1 1 ASN A 21 LYS A 26 1 6 HELIX 2 2 GLY A 43 GLU A 51 1 9 HELIX 3 3 PHE A 62 GLU A 71 1 10 HELIX 4 4 VAL A 101 LEU A 105 5 5 HELIX 5 5 ASP A 107 VAL A 115 1 9 HELIX 6 6 HIS A 134 ALA A 143 1 10 HELIX 7 7 THR A 163 ALA A 174 1 12 HELIX 8 8 HIS A 188 MSE A 190 5 3 HELIX 9 9 TYR A 191 TYR A 205 1 15 HELIX 10 10 GLY A 210 VAL A 216 1 7 SHEET 1 A 7 HIS A 75 LEU A 78 0 SHEET 2 A 7 ARG A 55 GLU A 60 1 N GLY A 58 O HIS A 75 SHEET 3 A 7 GLU A 34 ILE A 38 1 N ASP A 37 O SER A 57 SHEET 4 A 7 PHE A 93 GLY A 99 1 O ILE A 97 N LEU A 36 SHEET 5 A 7 ILE A 119 PRO A 130 1 O LEU A 126 N PHE A 98 SHEET 6 A 7 VAL A 217 LYS A 226 -1 O ILE A 222 N ALA A 127 SHEET 7 A 7 TYR A 176 TYR A 185 -1 N ASP A 182 O ILE A 221 LINK C THR A 83 N MSE A 84 1555 1555 1.32 LINK C MSE A 84 N ASP A 85 1555 1555 1.32 LINK C ASP A 85 N MSE A 86 1555 1555 1.33 LINK C MSE A 86 N PRO A 87 1555 1555 1.35 LINK C GLU A 166 N MSE A 167 1555 1555 1.33 LINK C MSE A 167 N LEU A 168 1555 1555 1.32 LINK C ARG A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N PHE A 171 1555 1555 1.32 LINK C LYS A 189 N MSE A 190 1555 1555 1.33 LINK C MSE A 190 N TYR A 191 1555 1555 1.33 LINK C PHE A 211 N MSE A 212 1555 1555 1.32 LINK C MSE A 212 N ALA A 213 1555 1555 1.33 LINK OE2 GLU A 103 NI B NI A 231 1555 1555 2.03 LINK NE2 HIS A 104 NI B NI A 231 1555 1555 2.36 LINK NE2 HIS A 104 NI A NI A 231 1555 1555 2.19 LINK NE2 HIS A 158 NI B NI A 231 1555 1555 2.18 LINK NE2 HIS A 188 NI NI A 230 1555 1555 2.33 LINK NI B NI A 231 O HOH A 365 1555 1555 2.47 LINK NI B NI A 231 O HOH A 382 1555 1555 2.03 LINK NI A NI A 231 O HOH A 384 1555 1555 2.50 LINK NI B NI A 231 O HOH A 384 1555 1555 1.90 LINK NI A NI A 231 O HOH A 385 1555 1555 2.28 LINK NI A NI A 231 O HOH A 405 1555 1555 2.25 SITE 1 AC1 5 HIS A 188 GLU A 192 HOH A 366 HOH A 367 SITE 2 AC1 5 HOH A 398 SITE 1 AC2 9 GLU A 103 HIS A 104 ASP A 155 HIS A 158 SITE 2 AC2 9 HOH A 365 HOH A 382 HOH A 384 HOH A 385 SITE 3 AC2 9 HOH A 405 CRYST1 91.223 54.399 52.751 90.00 109.50 90.00 C 1 2 1 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 0.010962 0.000000 0.003883 0.00000 SCALE2 0.000000 0.018383 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020111 0.00000