HEADER TRANSFERASE 17-OCT-05 2C49 TITLE CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE KINASE - TITLE 2 AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR KINASE MJ0406; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEOSIDE KINASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET17B; SOURCE 8 OTHER_DETAILS: METHANOCALDOCOCCUS JANNASCHII KEYWDS TRANSFERASE, NUCLEOSIDE KINASE, HYPERTHERMOPHILE, RIBOKINASE FAMILY, KEYWDS 2 RIBOKINASE FOLD EXPDTA X-RAY DIFFRACTION AUTHOR L.ARNFORS,T.HANSEN,W.MEINING,P.SCHOENHEIT,R.LADENSTEIN REVDAT 4 24-JUL-19 2C49 1 REMARK REVDAT 3 13-JUL-11 2C49 1 VERSN REVDAT 2 24-FEB-09 2C49 1 VERSN REVDAT 1 30-AUG-06 2C49 0 JRNL AUTH L.ARNFORS,T.HANSEN,P.SCHOENHEIT,R.LADENSTEIN,W.MEINING JRNL TITL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE JRNL TITL 2 KINASE: AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 62 1085 2006 JRNL REFN ISSN 0907-4449 JRNL PMID 16929110 JRNL DOI 10.1107/S0907444906024826 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 55509 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2955 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3739 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 193 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4731 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 104 REMARK 3 SOLVENT ATOMS : 162 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) : 21.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 1.26000 REMARK 3 B33 (A**2) : -1.64000 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): 0.181 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.803 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4982 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6777 ; 1.700 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 596 ; 7.538 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 727 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3749 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2331 ; 0.211 ; 0.200 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): 219 ; 0.159 ; 0.200 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): 35 ; 0.196 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.128 ; 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): 2971 ; 0.758 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4782 ; 1.264 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2011 ; 2.072 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1988 ; 2.989 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 15 4 REMARK 3 1 B 6 B 15 4 REMARK 3 2 A 42 A 97 4 REMARK 3 2 B 42 B 97 4 REMARK 3 3 A 115 A 297 4 REMARK 3 3 B 115 B 297 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1924 ; 0.44 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1924 ; 1.15 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 15 REMARK 3 RESIDUE RANGE : A 41 A 98 REMARK 3 RESIDUE RANGE : A 114 A 301 REMARK 3 ORIGIN FOR THE GROUP (A): 71.3506 22.8581 60.6100 REMARK 3 T TENSOR REMARK 3 T11: 0.0194 T22: 0.0105 REMARK 3 T33: 0.0655 T12: 0.0081 REMARK 3 T13: -0.0077 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 2.4540 L22: 1.8679 REMARK 3 L33: 2.9687 L12: -0.6070 REMARK 3 L13: 0.4665 L23: 0.2769 REMARK 3 S TENSOR REMARK 3 S11: 0.0232 S12: 0.1163 S13: 0.0207 REMARK 3 S21: -0.0744 S22: -0.0954 S23: 0.0044 REMARK 3 S31: -0.0685 S32: 0.1282 S33: 0.0722 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 40 REMARK 3 RESIDUE RANGE : A 99 A 113 REMARK 3 ORIGIN FOR THE GROUP (A): 71.3457 30.0739 39.1974 REMARK 3 T TENSOR REMARK 3 T11: 0.2009 T22: 0.1518 REMARK 3 T33: 0.1783 T12: -0.0200 REMARK 3 T13: -0.0427 T23: 0.0435 REMARK 3 L TENSOR REMARK 3 L11: 0.3299 L22: 3.3372 REMARK 3 L33: 5.4807 L12: -0.0792 REMARK 3 L13: -0.2342 L23: -1.2037 REMARK 3 S TENSOR REMARK 3 S11: -0.0367 S12: 0.2361 S13: 0.3473 REMARK 3 S21: -0.0043 S22: -0.0586 S23: -0.3196 REMARK 3 S31: -0.5942 S32: 0.4290 S33: 0.0952 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 15 REMARK 3 RESIDUE RANGE : B 41 B 98 REMARK 3 RESIDUE RANGE : B 114 B 300 REMARK 3 ORIGIN FOR THE GROUP (A): 58.8280 23.9438 12.0094 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.0335 REMARK 3 T33: 0.0978 T12: 0.0067 REMARK 3 T13: -0.0052 T23: -0.0352 REMARK 3 L TENSOR REMARK 3 L11: 1.7338 L22: 1.8826 REMARK 3 L33: 2.1245 L12: -0.1658 REMARK 3 L13: 0.3188 L23: -0.8849 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.1607 S13: 0.1099 REMARK 3 S21: -0.0860 S22: 0.0569 S23: 0.1399 REMARK 3 S31: -0.0371 S32: -0.0957 S33: -0.0529 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 40 REMARK 3 RESIDUE RANGE : B 99 B 113 REMARK 3 ORIGIN FOR THE GROUP (A): 59.5180 30.8366 38.0425 REMARK 3 T TENSOR REMARK 3 T11: 0.2495 T22: 0.1168 REMARK 3 T33: 0.1516 T12: 0.0793 REMARK 3 T13: -0.0234 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 1.6212 L22: 1.5116 REMARK 3 L33: 6.1729 L12: 0.6396 REMARK 3 L13: 0.6430 L23: 1.5639 REMARK 3 S TENSOR REMARK 3 S11: -0.0963 S12: 0.1594 S13: 0.3241 REMARK 3 S21: 0.0615 S22: -0.0025 S23: 0.1671 REMARK 3 S31: -0.5116 S32: -0.4866 S33: 0.0988 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2C49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1290026013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8098 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58526 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG4000, 0.10 M MGCL2, 0.1 M TRIS REMARK 280 -HCL PH 8.5 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 32.00300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.39200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.56550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.39200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.00300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.56550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 ILE A 302 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 ARG B 301 REMARK 465 ILE B 302 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 ASP A 202 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 209 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 68 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 140 CB - CG - OD2 ANGL. DEV. = 5.5 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 LYS A 4 -11.89 -148.75 REMARK 500 ASN A 29 49.07 71.86 REMARK 500 ASP A 68 58.44 -90.80 REMARK 500 PHE A 69 -60.84 -142.66 REMARK 500 ASN A 107 29.69 45.60 REMARK 500 THR A 138 -169.98 60.63 REMARK 500 ASN A 154 -70.63 -124.98 REMARK 500 LYS A 238 102.66 54.78 REMARK 500 LYS B 4 -31.12 -141.14 REMARK 500 GLU B 6 79.76 -60.11 REMARK 500 SER B 72 -150.49 -84.85 REMARK 500 ALA B 137 -164.12 -112.06 REMARK 500 ASN B 154 -64.81 -128.31 REMARK 500 LYS B 238 124.78 -177.48 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 PHE B 69 LYS B 70 -97.70 REMARK 500 LYS B 70 ASN B 71 147.32 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 A1302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2046 O REMARK 620 2 HOH A2056 O 90.5 REMARK 620 3 HOH A2057 O 90.7 87.4 REMARK 620 4 HOH A2066 O 88.8 88.3 175.7 REMARK 620 5 HOH A2077 O 90.9 177.8 94.2 90.1 REMARK 620 6 HOH A2079 O 177.9 91.3 90.6 90.0 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2054 O REMARK 620 2 HOH A2018 O 91.9 REMARK 620 3 HOH A2019 O 177.6 89.4 REMARK 620 4 HOH A2042 O 91.5 89.2 86.5 REMARK 620 5 HOH A2021 O 85.1 91.4 96.8 176.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2014 O REMARK 620 2 HOH B2082 O 90.7 REMARK 620 3 HOH B2041 O 89.7 179.2 REMARK 620 4 HOH B2081 O 179.8 89.5 90.1 REMARK 620 5 HOH B2053 O 90.5 88.0 91.3 89.5 REMARK 620 6 HOH B2040 O 90.0 90.5 90.2 90.0 178.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2036 O REMARK 620 2 HOH B2048 O 91.8 REMARK 620 3 HOH B2059 O 88.5 92.1 REMARK 620 4 HOH B2058 O 178.2 86.4 91.5 REMARK 620 5 HOH B2078 O 91.0 177.0 87.2 90.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADN A1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADN B1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP B1304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C4E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF METHANOCALDOCOCCUS JANNASCHII NUCLEOSIDE REMARK 900 KINASE - AN ARCHAEAL MEMBER OF THE RIBOKINASE FAMILY DBREF 2C49 A 1 302 UNP Q57849 Y406_METJA 1 302 DBREF 2C49 B 1 302 UNP Q57849 Y406_METJA 1 302 SEQRES 1 A 302 MET GLY GLY LYS MET GLU LYS ILE THR CYS VAL GLY HIS SEQRES 2 A 302 THR ALA LEU ASP TYR ILE PHE ASN VAL GLU LYS PHE PRO SEQRES 3 A 302 GLU PRO ASN THR SER ILE GLN ILE PRO SER ALA ARG LYS SEQRES 4 A 302 TYR TYR GLY GLY ALA ALA ALA ASN THR ALA VAL GLY ILE SEQRES 5 A 302 LYS LYS LEU GLY VAL ASN SER GLU LEU LEU SER CYS VAL SEQRES 6 A 302 GLY TYR ASP PHE LYS ASN SER GLY TYR GLU ARG TYR LEU SEQRES 7 A 302 LYS ASN LEU ASP ILE ASN ILE SER LYS LEU TYR TYR SER SEQRES 8 A 302 GLU GLU GLU GLU THR PRO LYS ALA TRP ILE PHE THR ASP SEQRES 9 A 302 LYS ASP ASN ASN GLN ILE THR PHE PHE LEU TRP GLY ALA SEQRES 10 A 302 ALA LYS HIS TYR LYS GLU LEU ASN PRO PRO ASN PHE ASN SEQRES 11 A 302 THR GLU ILE VAL HIS ILE ALA THR GLY ASP PRO GLU PHE SEQRES 12 A 302 ASN LEU LYS CYS ALA LYS LYS ALA TYR GLY ASN ASN LEU SEQRES 13 A 302 VAL SER PHE ASP PRO GLY GLN ASP LEU PRO GLN TYR SER SEQRES 14 A 302 LYS GLU MET LEU LEU GLU ILE ILE GLU HIS THR ASN PHE SEQRES 15 A 302 LEU PHE MET ASN LYS HIS GLU PHE GLU ARG ALA SER ASN SEQRES 16 A 302 LEU LEU ASN PHE GLU ILE ASP ASP TYR LEU GLU ARG VAL SEQRES 17 A 302 ASP ALA LEU ILE VAL THR LYS GLY SER LYS GLY SER VAL SEQRES 18 A 302 ILE TYR THR LYS ASP LYS LYS ILE GLU ILE PRO CYS ILE SEQRES 19 A 302 LYS ALA GLY LYS VAL ILE ASP PRO THR GLY ALA GLY ASP SEQRES 20 A 302 SER TYR ARG ALA GLY PHE LEU SER ALA TYR VAL LYS GLY SEQRES 21 A 302 TYR ASP LEU GLU LYS CYS GLY LEU ILE GLY ALA ALA THR SEQRES 22 A 302 ALA SER PHE VAL VAL GLU ALA LYS GLY CYS GLN THR ASN SEQRES 23 A 302 LEU PRO THR TRP ASP LYS VAL VAL GLU ARG LEU GLU LYS SEQRES 24 A 302 HIS ARG ILE SEQRES 1 B 302 MET GLY GLY LYS MET GLU LYS ILE THR CYS VAL GLY HIS SEQRES 2 B 302 THR ALA LEU ASP TYR ILE PHE ASN VAL GLU LYS PHE PRO SEQRES 3 B 302 GLU PRO ASN THR SER ILE GLN ILE PRO SER ALA ARG LYS SEQRES 4 B 302 TYR TYR GLY GLY ALA ALA ALA ASN THR ALA VAL GLY ILE SEQRES 5 B 302 LYS LYS LEU GLY VAL ASN SER GLU LEU LEU SER CYS VAL SEQRES 6 B 302 GLY TYR ASP PHE LYS ASN SER GLY TYR GLU ARG TYR LEU SEQRES 7 B 302 LYS ASN LEU ASP ILE ASN ILE SER LYS LEU TYR TYR SER SEQRES 8 B 302 GLU GLU GLU GLU THR PRO LYS ALA TRP ILE PHE THR ASP SEQRES 9 B 302 LYS ASP ASN ASN GLN ILE THR PHE PHE LEU TRP GLY ALA SEQRES 10 B 302 ALA LYS HIS TYR LYS GLU LEU ASN PRO PRO ASN PHE ASN SEQRES 11 B 302 THR GLU ILE VAL HIS ILE ALA THR GLY ASP PRO GLU PHE SEQRES 12 B 302 ASN LEU LYS CYS ALA LYS LYS ALA TYR GLY ASN ASN LEU SEQRES 13 B 302 VAL SER PHE ASP PRO GLY GLN ASP LEU PRO GLN TYR SER SEQRES 14 B 302 LYS GLU MET LEU LEU GLU ILE ILE GLU HIS THR ASN PHE SEQRES 15 B 302 LEU PHE MET ASN LYS HIS GLU PHE GLU ARG ALA SER ASN SEQRES 16 B 302 LEU LEU ASN PHE GLU ILE ASP ASP TYR LEU GLU ARG VAL SEQRES 17 B 302 ASP ALA LEU ILE VAL THR LYS GLY SER LYS GLY SER VAL SEQRES 18 B 302 ILE TYR THR LYS ASP LYS LYS ILE GLU ILE PRO CYS ILE SEQRES 19 B 302 LYS ALA GLY LYS VAL ILE ASP PRO THR GLY ALA GLY ASP SEQRES 20 B 302 SER TYR ARG ALA GLY PHE LEU SER ALA TYR VAL LYS GLY SEQRES 21 B 302 TYR ASP LEU GLU LYS CYS GLY LEU ILE GLY ALA ALA THR SEQRES 22 B 302 ALA SER PHE VAL VAL GLU ALA LYS GLY CYS GLN THR ASN SEQRES 23 B 302 LEU PRO THR TRP ASP LYS VAL VAL GLU ARG LEU GLU LYS SEQRES 24 B 302 HIS ARG ILE HET ADN A1301 19 HET MG A1302 1 HET MG A1303 1 HET ANP A1304 31 HET ADN B1301 19 HET MG B1302 1 HET MG B1303 1 HET ANP B1304 31 HETNAM ADN ADENOSINE HETNAM MG MAGNESIUM ION HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 3 ADN 2(C10 H13 N5 O4) FORMUL 4 MG 4(MG 2+) FORMUL 6 ANP 2(C10 H17 N6 O12 P3) FORMUL 11 HOH *162(H2 O) HELIX 1 1 GLY A 43 LEU A 55 1 13 HELIX 2 2 SER A 72 LEU A 81 1 10 HELIX 3 3 GLY A 116 LEU A 124 5 9 HELIX 4 4 ASP A 140 TYR A 152 1 13 HELIX 5 5 PRO A 161 TYR A 168 5 8 HELIX 6 6 SER A 169 GLU A 178 1 10 HELIX 7 7 ASN A 186 ASN A 198 1 13 HELIX 8 8 GLU A 200 GLU A 206 1 7 HELIX 9 9 GLY A 216 LYS A 218 5 3 HELIX 10 10 GLY A 244 LYS A 259 1 16 HELIX 11 11 ASP A 262 VAL A 278 1 17 HELIX 12 12 THR A 289 HIS A 300 1 12 HELIX 13 13 GLY B 43 LEU B 55 1 13 HELIX 14 14 SER B 72 LEU B 81 1 10 HELIX 15 15 GLY B 116 LEU B 124 5 9 HELIX 16 16 ASP B 140 TYR B 152 1 13 HELIX 17 17 PRO B 161 TYR B 168 5 8 HELIX 18 18 SER B 169 HIS B 179 1 11 HELIX 19 19 LYS B 187 ASN B 198 1 12 HELIX 20 20 GLU B 200 GLU B 206 1 7 HELIX 21 21 GLY B 216 LYS B 218 5 3 HELIX 22 22 GLY B 244 LYS B 259 1 16 HELIX 23 23 ASP B 262 VAL B 278 1 17 HELIX 24 24 THR B 289 HIS B 300 1 12 SHEET 1 AA 8 ASN A 58 LEU A 62 0 SHEET 2 AA 8 MET A 5 VAL A 11 1 O GLU A 6 N ASN A 58 SHEET 3 AA 8 THR A 131 ALA A 137 1 N GLU A 132 O MET A 5 SHEET 4 AA 8 LEU A 156 ASP A 160 1 O LEU A 156 N VAL A 134 SHEET 5 AA 8 PHE A 182 MET A 185 1 O PHE A 182 N PHE A 159 SHEET 6 AA 8 ALA A 210 THR A 214 1 O ALA A 210 N LEU A 183 SHEET 7 AA 8 SER A 220 TYR A 223 -1 O VAL A 221 N VAL A 213 SHEET 8 AA 8 LYS A 228 ILE A 231 -1 O ILE A 229 N ILE A 222 SHEET 1 AB 5 LYS A 39 GLY A 42 0 SHEET 2 AB 5 ALA A 15 ASN A 21 -1 O ALA A 15 N GLY A 42 SHEET 3 AB 5 LYS A 98 THR A 103 1 O ALA A 99 N TYR A 18 SHEET 4 AB 5 GLN A 109 LEU A 114 -1 O ILE A 110 N PHE A 102 SHEET 5 AB 5 SER B 31 ILE B 34 1 O ILE B 32 N PHE A 113 SHEET 1 AC 5 THR A 30 ILE A 34 0 SHEET 2 AC 5 GLN B 109 LEU B 114 1 O THR B 111 N ILE A 32 SHEET 3 AC 5 LYS B 98 THR B 103 -1 O LYS B 98 N LEU B 114 SHEET 4 AC 5 ALA B 15 ASN B 21 1 O LEU B 16 N ALA B 99 SHEET 5 AC 5 ARG B 38 GLY B 42 -1 O ARG B 38 N ILE B 19 SHEET 1 AD 2 CYS A 64 VAL A 65 0 SHEET 2 AD 2 TYR A 89 TYR A 90 1 O TYR A 89 N VAL A 65 SHEET 1 BA 8 ASN B 58 LEU B 62 0 SHEET 2 BA 8 MET B 5 VAL B 11 1 O GLU B 6 N ASN B 58 SHEET 3 BA 8 THR B 131 ILE B 136 1 N GLU B 132 O LYS B 7 SHEET 4 BA 8 LEU B 156 PHE B 159 1 O LEU B 156 N VAL B 134 SHEET 5 BA 8 PHE B 182 ASN B 186 1 O PHE B 182 N PHE B 159 SHEET 6 BA 8 ALA B 210 THR B 214 1 O ALA B 210 N LEU B 183 SHEET 7 BA 8 SER B 220 TYR B 223 -1 O VAL B 221 N VAL B 213 SHEET 8 BA 8 LYS B 228 ILE B 231 -1 O ILE B 229 N ILE B 222 SHEET 1 BB 2 CYS B 64 VAL B 65 0 SHEET 2 BB 2 TYR B 89 TYR B 90 1 O TYR B 89 N VAL B 65 LINK MG MG A1302 O HOH A2046 1555 1555 2.16 LINK MG MG A1302 O HOH A2056 1555 1555 2.15 LINK MG MG A1302 O HOH A2057 1555 1555 2.17 LINK MG MG A1302 O HOH A2066 1555 1555 2.18 LINK MG MG A1302 O HOH A2077 1555 1555 2.18 LINK MG MG A1302 O HOH A2079 1555 1555 2.15 LINK MG MG A1303 O HOH A2054 1555 1555 2.16 LINK MG MG A1303 O HOH A2018 1555 1555 2.19 LINK MG MG A1303 O HOH A2019 1555 1555 2.18 LINK MG MG A1303 O HOH A2042 1555 1555 2.16 LINK MG MG A1303 O HOH A2021 1555 1555 2.18 LINK MG MG B1302 O HOH B2014 1555 1555 2.18 LINK MG MG B1302 O HOH B2082 1555 1555 2.17 LINK MG MG B1302 O HOH B2041 1555 1555 2.17 LINK MG MG B1302 O HOH B2081 1555 1555 2.17 LINK MG MG B1302 O HOH B2053 1555 1555 2.18 LINK MG MG B1302 O HOH B2040 1555 1555 2.18 LINK MG MG B1303 O HOH B2036 1555 1555 2.19 LINK MG MG B1303 O HOH B2048 1555 1555 2.17 LINK MG MG B1303 O HOH B2059 1555 1555 2.17 LINK MG MG B1303 O HOH B2058 1555 1555 2.17 LINK MG MG B1303 O HOH B2078 1555 4555 2.19 SITE 1 AC1 6 HOH A2046 HOH A2056 HOH A2057 HOH A2066 SITE 2 AC1 6 HOH A2077 HOH A2079 SITE 1 AC2 5 HOH A2018 HOH A2019 HOH A2021 HOH A2042 SITE 2 AC2 5 HOH A2054 SITE 1 AC3 6 HOH B2014 HOH B2040 HOH B2041 HOH B2053 SITE 2 AC3 6 HOH B2081 HOH B2082 SITE 1 AC4 5 HOH B2036 HOH B2048 HOH B2058 HOH B2059 SITE 2 AC4 5 HOH B2078 SITE 1 AC5 16 HIS A 13 ALA A 15 ASP A 17 GLY A 42 SITE 2 AC5 16 GLY A 43 ASN A 47 THR A 111 PHE A 113 SITE 3 AC5 16 GLN A 163 ASP A 164 ASP A 247 CYS A 283 SITE 4 AC5 16 HOH A2077 HOH A2078 SER B 31 GLN B 33 SITE 1 AC6 16 GLN A 109 ASN A 186 THR A 214 GLY A 216 SITE 2 AC6 16 GLY A 219 CYS A 233 ILE A 234 VAL A 239 SITE 3 AC6 16 THR A 243 ALA A 245 GLY A 246 ALA A 274 SITE 4 AC6 16 HOH A2062 HOH A2072 HOH A2079 HOH A2080 SITE 1 AC7 7 HIS B 13 ALA B 15 ASP B 17 GLY B 42 SITE 2 AC7 7 GLY B 43 ALA B 44 HOH B2080 SITE 1 AC8 19 ASN B 186 THR B 214 LYS B 215 GLY B 216 SITE 2 AC8 19 GLY B 219 CYS B 233 ILE B 234 VAL B 239 SITE 3 AC8 19 PRO B 242 THR B 243 GLY B 244 ALA B 245 SITE 4 AC8 19 GLY B 246 TYR B 249 ARG B 250 ALA B 274 SITE 5 AC8 19 HOH B2060 HOH B2081 HOH B2082 CRYST1 64.006 83.131 146.784 90.00 90.00 90.00 P 21 21 21 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 0.015624 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006813 0.00000 MTRIX1 1 -0.996080 0.032971 0.082070 130.16000 1 MTRIX2 1 0.023822 0.993640 -0.110060 -1.78790 1 MTRIX3 1 -0.085177 -0.107670 -0.990530 70.50800 1