HEADER METAL BINDING PROTEIN 05-FEB-07 2OSD TITLE CRYSTAL STRUCTURE OF A VINYL-4-REDUCTASE FAMILY PROTEIN (MJ_1460) FROM TITLE 2 METHANOCALDOCOCCUS JANNASCHII DSM AT 2.40 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN MJ1460; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: V4R DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII DSM 2661; SOURCE 3 ORGANISM_TAXID: 243232; SOURCE 4 STRAIN: DSM 2661, JAL-1, JCM 10045, NBRC 100440; SOURCE 5 ATCC: 43067; SOURCE 6 GENE: 1592102, MJ1460; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 25-JAN-23 2OSD 1 SEQADV REVDAT 6 20-OCT-21 2OSD 1 REMARK SEQADV LINK REVDAT 5 18-OCT-17 2OSD 1 REMARK REVDAT 4 13-JUL-11 2OSD 1 VERSN REVDAT 3 23-MAR-11 2OSD 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 2OSD 1 VERSN REVDAT 1 20-FEB-07 2OSD 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN MJ_1460 (1592102) JRNL TITL 2 FROM METHANOCOCCUS JANNASCHII AT 2.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8895 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) : 0.219 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 421 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 603 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1177 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.43000 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): 0.305 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.198 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.426 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1234 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 845 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1665 ; 1.574 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2078 ; 0.962 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 152 ; 6.220 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 54 ;40.617 ;25.926 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 211 ;19.236 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ;31.953 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 181 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1355 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 237 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 241 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 777 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 587 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 647 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 41 ; 0.189 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.323 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 18 ; 0.375 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.183 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.113 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 2 ; 0.137 ; 0.200 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): 790 ; 2.223 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 302 ; 0.446 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1232 ; 3.526 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 512 ; 6.368 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 432 ; 7.963 ;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 5 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6960 4.8495 28.4007 REMARK 3 T TENSOR REMARK 3 T11: -0.1232 T22: -0.3418 REMARK 3 T33: -0.2538 T12: -0.0169 REMARK 3 T13: -0.0221 T23: -0.0440 REMARK 3 L TENSOR REMARK 3 L11: 3.7316 L22: 4.8298 REMARK 3 L33: 5.0290 L12: 0.0404 REMARK 3 L13: 0.1906 L23: 1.3634 REMARK 3 S TENSOR REMARK 3 S11: -0.1126 S12: 0.0910 S13: 0.3192 REMARK 3 S21: -0.2104 S22: 0.1143 S23: -0.1761 REMARK 3 S31: -0.5322 S32: 0.3015 S33: -0.0017 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 RIDING POSITIONS. REMARK 3 2. ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. REMARK 3 4. RESIDUES 45-46 ARE DISORDERED AND NOT VISIBLE REMARK 3 IN THE ELECTRON DENSITY MAPS. THEY WERE NOT MODELED. REMARK 3 5. TWO CA, THREE ETHYLENE GLYCOL MOLECULES, ONE CL ION FROM THE REMARK 3 CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. REMARK 3 6. A ZN ATOM OF THE SUBUNIT IN THE ASYMMETRIC UNIT REMARK 3 IS COORDINATED TO THE SIDE CHAINS OF HIS 116, GLU 139, REMARK 3 CYS 142 AND CYS 150. X-RAY FLUORESCENCE EXPERIMENTS SUPPORT REMARK 3 THE ASSIGNMENT OF THE ZINC ION. REMARK 4 REMARK 4 2OSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91837, 0.97879, 0.97908 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 (HORIZONTAL FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) 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, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8939 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.748 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.08400 REMARK 200 FOR THE DATA SET : 6.6000 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) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.91700 REMARK 200 R SYM FOR SHELL (I) : 0.91700 REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 0.2M CACL2, 20.0% PEG 3350, REMARK 280 NO BUFFER, PH 5.1, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 59.49500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.89300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.89300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.24250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.89300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.89300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.74750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.89300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.89300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 89.24250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.89300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.89300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.74750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.49500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.49500 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 ALA A 2 REMARK 465 PHE A 3 REMARK 465 MSE A 4 REMARK 465 GLU A 45 REMARK 465 LEU A 46 REMARK 465 VAL A 157 REMARK 465 ASP A 158 REMARK 465 GLU A 159 REMARK 465 LEU A 160 REMARK 465 ASN A 161 REMARK 465 LYS A 162 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 5 CG CD OE1 OE2 REMARK 470 LYS A 6 CG CD CE NZ REMARK 470 LYS A 22 CE NZ REMARK 470 LYS A 42 CE NZ REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 SER A 48 OG REMARK 470 LYS A 66 CD CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 76 CE NZ REMARK 470 ASN A 88 OD1 ND2 REMARK 470 LYS A 89 CD CE NZ REMARK 470 ILE A 90 CG1 CD1 REMARK 470 LEU A 91 CG CD1 CD2 REMARK 470 LEU A 92 CG CD1 CD2 REMARK 470 LYS A 93 CG CD CE NZ REMARK 470 ASN A 94 OD1 ND2 REMARK 470 LYS A 111 NZ REMARK 470 GLU A 112 OE1 OE2 REMARK 470 GLU A 113 OE1 OE2 REMARK 470 GLU A 153 OE1 REMARK 470 LYS A 155 CD CE NZ 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 MSE A 62 CG - SE - CE ANGL. DEV. = -14.4 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 64 68.54 36.52 REMARK 500 ASN A 79 36.05 78.88 REMARK 500 LEU A 92 -77.48 -71.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 163 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 19 OE1 REMARK 620 2 GLU A 19 OE2 53.3 REMARK 620 3 GLU A 128 OE2 114.9 162.1 REMARK 620 4 GLU A 129 OE2 127.8 77.5 107.6 REMARK 620 5 HOH A 183 O 74.8 79.9 84.0 81.3 REMARK 620 6 HOH A 184 O 101.1 122.9 69.8 121.5 149.0 REMARK 620 7 HOH A 186 O 112.3 78.2 119.6 66.8 144.4 66.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 164 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 19 OE2 REMARK 620 2 GLU A 23 OE2 85.9 REMARK 620 3 GLU A 23 OE1 84.0 49.3 REMARK 620 4 GLU A 129 OE2 74.3 151.0 144.8 REMARK 620 5 GLU A 129 OE1 123.7 144.8 141.4 49.4 REMARK 620 6 HOH A 181 O 157.6 73.6 75.9 128.0 78.6 REMARK 620 7 HOH A 193 O 92.8 86.9 136.1 73.4 74.2 94.9 REMARK 620 8 HOH A 198 O 99.9 120.2 72.0 84.7 76.6 83.2 150.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 166 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 116 ND1 REMARK 620 2 GLU A 139 OE2 115.3 REMARK 620 3 CYS A 142 SG 103.3 106.4 REMARK 620 4 CYS A 150 SG 109.6 104.5 118.2 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 CA A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 169 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 373077 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2OSO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII DSM 2661 REMARK 900 COMPLETE GENOME (1592102) FROM METHANOCOCCUS JANNASCHII AT 1.90 A REMARK 900 RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 1. 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. REMARK 999 2. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING REMARK 999 MUTATIONS: K132Y, K133Y AND K134Y DBREF 2OSD A 1 162 UNP Q58855 Y1460_METJA 1 162 SEQADV 2OSD GLY A 0 UNP Q58855 EXPRESSION TAG SEQADV 2OSD MSE A 1 UNP Q58855 MET 1 MODIFIED RESIDUE SEQADV 2OSD MSE A 4 UNP Q58855 MET 4 MODIFIED RESIDUE SEQADV 2OSD MSE A 29 UNP Q58855 MET 29 MODIFIED RESIDUE SEQADV 2OSD MSE A 62 UNP Q58855 MET 62 MODIFIED RESIDUE SEQADV 2OSD MSE A 78 UNP Q58855 MET 78 MODIFIED RESIDUE SEQADV 2OSD TYR A 132 UNP Q58855 LYS 132 ENGINEERED MUTATION SEQADV 2OSD TYR A 133 UNP Q58855 LYS 133 ENGINEERED MUTATION SEQADV 2OSD TYR A 134 UNP Q58855 LYS 134 ENGINEERED MUTATION SEQRES 1 A 163 GLY MSE ALA PHE MSE GLU LYS ILE PHE PRO ASP ILE LEU SEQRES 2 A 163 GLU ALA ILE ARG ASN GLU GLU ILE ILE LYS GLU SER LYS SEQRES 3 A 163 LYS ILE PRO MSE PRO TYR PHE GLY LEU PHE ALA LEU VAL SEQRES 4 A 163 ILE PHE ASP LYS VAL LYS GLU LEU GLY SER GLU THR SER SEQRES 5 A 163 LEU TYR GLU ILE GLY GLU GLU PHE GLY LYS MSE LEU SER SEQRES 6 A 163 PRO LYS ASN ILE GLU GLU LEU LYS LYS ILE PHE LYS LEU SEQRES 7 A 163 MSE ASN PHE GLY ASP LEU GLU ILE ASP GLU ASN LYS ILE SEQRES 8 A 163 LEU LEU LYS ASN PRO PRO TYR LYS ILE LYS LEU SER ASN SEQRES 9 A 163 PRO PRO TYR GLN TRP VAL SER LYS GLU GLU PRO ILE HIS SEQRES 10 A 163 ASP PHE ILE ALA GLY ILE LEU ALA GLY CYS LEU GLU GLU SEQRES 11 A 163 ILE PHE TYR TYR TYR PHE VAL VAL ASN GLU VAL GLU CYS SEQRES 12 A 163 VAL SER GLN GLY LYS ASP LYS CYS VAL PHE GLU VAL LYS SEQRES 13 A 163 GLU VAL ASP GLU LEU ASN LYS MODRES 2OSD MSE A 29 MET SELENOMETHIONINE MODRES 2OSD MSE A 62 MET SELENOMETHIONINE MODRES 2OSD MSE A 78 MET SELENOMETHIONINE HET MSE A 29 8 HET MSE A 62 8 HET MSE A 78 8 HET CA A 163 1 HET CA A 164 1 HET CL A 165 1 HET ZN A 166 1 HET EDO A 167 4 HET EDO A 168 4 HET EDO A 169 4 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 CA 2(CA 2+) FORMUL 4 CL CL 1- FORMUL 5 ZN ZN 2+ FORMUL 6 EDO 3(C2 H6 O2) FORMUL 9 HOH *30(H2 O) HELIX 1 1 ILE A 7 ASN A 17 1 11 HELIX 2 2 ASN A 17 SER A 24 1 8 HELIX 3 3 PRO A 28 LYS A 44 1 17 HELIX 4 4 SER A 51 SER A 64 1 14 HELIX 5 5 ASN A 67 ASN A 79 1 13 HELIX 6 6 ASP A 86 LEU A 92 1 7 HELIX 7 7 HIS A 116 TYR A 132 1 17 HELIX 8 8 CYS A 142 GLY A 146 5 5 SHEET 1 A 4 ASP A 82 GLU A 84 0 SHEET 2 A 4 TYR A 97 SER A 102 -1 O LYS A 100 N GLU A 84 SHEET 3 A 4 CYS A 150 LYS A 155 -1 O PHE A 152 N ILE A 99 SHEET 4 A 4 VAL A 136 GLU A 141 -1 N ASN A 138 O GLU A 153 LINK C PRO A 28 N MSE A 29 1555 1555 1.32 LINK C MSE A 29 N PRO A 30 1555 1555 1.34 LINK C LYS A 61 N MSE A 62 1555 1555 1.32 LINK C MSE A 62 N LEU A 63 1555 1555 1.33 LINK C LEU A 77 N MSE A 78 1555 1555 1.33 LINK C MSE A 78 N ASN A 79 1555 1555 1.33 LINK OE1 GLU A 19 CA CA A 163 5555 1555 2.62 LINK OE2 GLU A 19 CA CA A 163 5555 1555 2.39 LINK OE2 GLU A 19 CA CA A 164 5555 1555 2.47 LINK OE2 GLU A 23 CA CA A 164 5555 1555 2.23 LINK OE1 GLU A 23 CA CA A 164 5555 1555 2.84 LINK ND1 HIS A 116 ZN ZN A 166 1555 1555 2.13 LINK OE2 GLU A 128 CA CA A 163 1555 1555 1.97 LINK OE2 GLU A 129 CA CA A 163 1555 1555 2.56 LINK OE2 GLU A 129 CA CA A 164 1555 1555 2.65 LINK OE1 GLU A 129 CA CA A 164 1555 1555 2.60 LINK OE2 GLU A 139 ZN ZN A 166 1555 1555 2.06 LINK SG CYS A 142 ZN ZN A 166 1555 1555 2.38 LINK SG CYS A 150 ZN ZN A 166 1555 1555 2.02 LINK CA CA A 163 O HOH A 183 1555 1555 2.46 LINK CA CA A 163 O HOH A 184 1555 1555 2.55 LINK CA CA A 163 O HOH A 186 1555 1555 2.08 LINK CA CA A 164 O HOH A 181 1555 1555 2.51 LINK CA CA A 164 O HOH A 193 1555 1555 2.23 LINK CA CA A 164 O HOH A 198 1555 1555 2.17 CISPEP 1 PRO A 95 PRO A 96 0 -8.62 SITE 1 AC1 6 GLU A 19 GLU A 128 GLU A 129 HOH A 183 SITE 2 AC1 6 HOH A 184 HOH A 186 SITE 1 AC2 6 GLU A 19 GLU A 23 GLU A 129 HOH A 181 SITE 2 AC2 6 HOH A 193 HOH A 198 SITE 1 AC3 5 SER A 24 LYS A 25 MSE A 29 TYR A 106 SITE 2 AC3 5 HOH A 190 SITE 1 AC4 4 HIS A 116 GLU A 139 CYS A 142 CYS A 150 SITE 1 AC5 2 PHE A 32 TYR A 106 SITE 1 AC6 3 SER A 64 PRO A 65 GLU A 129 SITE 1 AC7 2 ASN A 138 GLU A 139 CRYST1 55.786 55.786 118.990 90.00 90.00 90.00 P 43 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 0.017930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008400 0.00000