HEADER CAPPING ENZYME 20-APR-97 1CKN TITLE STRUCTURE OF GUANYLYLATED MRNA CAPPING ENZYME COMPLEXED WITH GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA CAPPING ENZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNA GUANYLYLTRANSFERASE; COMPND 5 EC: 2.7.7.50; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MRNA CAPPING ENZYME; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: RNA GUANYLYLTRANSFERASE; COMPND 11 EC: 2.7.7.50; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARAMECIUM BURSARIA CHLORELLA VIRUS 1; SOURCE 3 ORGANISM_TAXID: 10506; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: PARAMECIUM BURSARIA CHLORELLA VIRUS 1; SOURCE 8 ORGANISM_TAXID: 10506; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MRNA, CAPPING ENZYME, NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.HAKANSSON,A.J.DOHERTY,D.B.WIGLEY REVDAT 3 09-AUG-23 1CKN 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1CKN 1 VERSN REVDAT 1 07-JUL-97 1CKN 0 JRNL AUTH K.HAKANSSON,A.J.DOHERTY,S.SHUMAN,D.B.WIGLEY JRNL TITL X-RAY CRYSTALLOGRAPHY REVEALS A LARGE CONFORMATIONAL CHANGE JRNL TITL 2 DURING GUANYL TRANSFER BY MRNA CAPPING ENZYMES. JRNL REF CELL(CAMBRIDGE,MASS.) V. 89 545 1997 JRNL REFN ISSN 0092-8674 JRNL PMID 9160746 JRNL DOI 10.1016/S0092-8674(00)80236-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.J.DOHERTY,K.HAKANSSON,C.K.HO,S.SHUMAN,D.B.WIGLEY REMARK 1 TITL CRYSTALLIZATION OF THE RNA GUANYLYLTRANSFERASE OF CHLORELLA REMARK 1 TITL 2 VIRUS PBCV-1 CHANGE DURING GUANYL TRANSFER BY MRNA CAPPING REMARK 1 TITL 3 ENZYMES REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 35375 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 342 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 2.798 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.17 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.242 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM19.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : USER DEFINED REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19.PEP REMARK 3 TOPOLOGY FILE 2 : USER DEFINED REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172362. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JAN-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36109 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1CKM REMARK 200 REMARK 200 REMARK: THE POLYPEPTIDE CHAIN OF 1CKM WAS USED AS INITIAL MODEL. REMARK 200 THE SAME SELECTION OF DATA FOR MONITORING THE FREE R WAS USED. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR DIFFUSION. 10-15 REMARK 280 MG/ML PROTEIN IN 50 MM TRIS-HCL, 0.5 M NACL, 10 MM MGCL2, 5MM REMARK 280 GTP, 2 MM EDTA, 4 MM DTT, PH 7.5 WERE MIXED WITH AN EQUAL VOLUME REMARK 280 OF AND EQUILIBRATED AGAINST 100 MM TRIS- HCL, 200 MM NACL, 200 REMARK 280 MM AMMONIUM SULFATE, 34% MEOPEG 5000, PH 7.5. THE CRYSTALS WERE REMARK 280 SOAKED IN EQUILIBRATION SOLUTION WITH 100 MM MANGANESE(II) REMARK 280 CHLORIDE AND 5 MM GTP FOR 4 HOURS PRIOR TO DATA COLLECTION., REMARK 280 VAPOR DIFFUSION - HANGING DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 52.50800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.50800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 47.45300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 106.47650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.45300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 106.47650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.50800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.45300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 106.47650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.50800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.45300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 106.47650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 -1.000000 0.000000 0.000000 94.90600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.50800 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE IN DIFFERENT REMARK 400 CONFORMATIONS. THE PROTEIN IS MONOMERIC AND THIS ENTRY REMARK 400 MERELY REPRESENTS A CO-CRYSTAL OF THE ENZYME IN TWO REMARK 400 DIFFERENT CONFORMATIONS. THE ACTIVE SITE LYSINE (B 82) REMARK 400 IS GUANYLYLATED ONLY IN MOLECULE B. GTP IS NON-COVALENTLY REMARK 400 BOUND TO THE ACTIVE SITE IN MOLECULE A. 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 VAL A 2 REMARK 465 PRO A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 ILE A 6 REMARK 465 ASN A 7 REMARK 465 THR A 8 REMARK 465 GLY A 9 REMARK 465 LYS A 10 REMARK 465 LYS A 328 REMARK 465 TRP A 329 REMARK 465 GLU A 330 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 PRO B 3 REMARK 465 PRO B 4 REMARK 465 THR B 5 REMARK 465 ILE B 6 REMARK 465 ASN B 7 REMARK 465 THR B 8 REMARK 465 GLY B 9 REMARK 465 LYS B 10 REMARK 465 LYS B 328 REMARK 465 TRP B 329 REMARK 465 GLU B 330 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 HIS A 29 NE2 HIS A 29 CD2 -0.068 REMARK 500 HIS A 51 NE2 HIS A 51 CD2 -0.088 REMARK 500 HIS A 195 NE2 HIS A 195 CD2 -0.072 REMARK 500 HIS A 202 NE2 HIS A 202 CD2 -0.067 REMARK 500 HIS A 211 NE2 HIS A 211 CD2 -0.079 REMARK 500 HIS A 241 NE2 HIS A 241 CD2 -0.075 REMARK 500 HIS B 29 NE2 HIS B 29 CD2 -0.075 REMARK 500 HIS B 51 NE2 HIS B 51 CD2 -0.067 REMARK 500 HIS B 195 NE2 HIS B 195 CD2 -0.066 REMARK 500 HIS B 202 NE2 HIS B 202 CD2 -0.067 REMARK 500 HIS B 240 NE2 HIS B 240 CD2 -0.082 REMARK 500 HIS B 241 NE2 HIS B 241 CD2 -0.078 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 164 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 170 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 TRP A 190 CD1 - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 TRP A 190 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 HIS A 241 CB - CG - CD2 ANGL. DEV. = -10.2 DEGREES REMARK 500 TRP A 289 CD1 - CG - CD2 ANGL. DEV. = 7.4 DEGREES REMARK 500 TRP A 289 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 55 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 87 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 87 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 106 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 106 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 120 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 VAL B 150 CG1 - CB - CG2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 164 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 164 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 170 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR B 187 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TRP B 190 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP B 190 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 VAL B 267 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 TRP B 289 CD1 - CG - CD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 TRP B 289 CB - CG - CD1 ANGL. DEV. = -7.8 DEGREES REMARK 500 TRP B 289 CE2 - CD2 - CG ANGL. DEV. = -7.4 DEGREES REMARK 500 TRP B 289 CG - CD2 - CE3 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 304 NE - CZ - NH1 ANGL. DEV. = 3.5 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 THR A 93 -168.31 -161.35 REMARK 500 MET A 108 36.92 75.43 REMARK 500 ASN A 117 37.81 -87.22 REMARK 500 HIS A 195 55.01 -117.35 REMARK 500 PRO A 237 108.32 -58.42 REMARK 500 HIS A 240 55.76 -92.88 REMARK 500 ASP A 286 63.17 39.93 REMARK 500 ASN B 117 42.44 -90.83 REMARK 500 SER B 152 32.60 38.71 REMARK 500 HIS B 195 69.54 -113.57 REMARK 500 GLU B 250 -39.98 -26.35 REMARK 500 ILE B 292 -61.63 -97.47 REMARK 500 ASN B 299 -6.04 -143.57 REMARK 500 ASN B 317 79.23 -110.22 REMARK 500 LEU B 324 22.10 -79.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 98 0.08 SIDE CHAIN REMARK 500 TYR A 111 0.08 SIDE CHAIN REMARK 500 ARG A 170 0.08 SIDE CHAIN REMARK 500 TYR A 274 0.09 SIDE CHAIN REMARK 500 ARG A 295 0.10 SIDE CHAIN REMARK 500 TYR B 77 0.11 SIDE CHAIN REMARK 500 ARG B 106 0.16 SIDE CHAIN REMARK 500 TYR B 111 0.07 SIDE CHAIN REMARK 500 TYR B 187 0.07 SIDE CHAIN REMARK 500 TYR B 273 0.09 SIDE CHAIN REMARK 500 TYR B 274 0.09 SIDE CHAIN 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 MN B1001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GPL B 82 O1P REMARK 620 2 HOH B1121 O 74.8 REMARK 620 3 HOH B1122 O 89.2 78.4 REMARK 620 4 HOH B1163 O 149.3 75.8 76.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: GMA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE LYSINE. REMARK 800 REMARK 800 SITE_IDENTIFIER: GMB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE LYSINE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 899 DBREF 1CKN A 1 330 UNP Q84424 MCE_9PHYC 1 330 DBREF 1CKN B 1 330 UNP Q84424 MCE_9PHYC 1 330 SEQADV 1CKN GPL B 82 UNP Q84424 LYS 82 CONFLICT SEQRES 1 A 330 MET VAL PRO PRO THR ILE ASN THR GLY LYS ASN ILE THR SEQRES 2 A 330 THR GLU ARG ALA VAL LEU THR LEU ASN GLY LEU GLN ILE SEQRES 3 A 330 LYS LEU HIS LYS VAL VAL GLY GLU SER ARG ASP ASP ILE SEQRES 4 A 330 VAL ALA LYS MET LYS ASP LEU ALA MET ASP ASP HIS LYS SEQRES 5 A 330 PHE PRO ARG LEU PRO GLY PRO ASN PRO VAL SER ILE GLU SEQRES 6 A 330 ARG LYS ASP PHE GLU LYS LEU LYS GLN ASN LYS TYR VAL SEQRES 7 A 330 VAL SER GLU LYS THR ASP GLY ILE ARG PHE MET MET PHE SEQRES 8 A 330 PHE THR ARG VAL PHE GLY PHE LYS VAL CYS THR ILE ILE SEQRES 9 A 330 ASP ARG ALA MET THR VAL TYR LEU LEU PRO PHE LYS ASN SEQRES 10 A 330 ILE PRO ARG VAL LEU PHE GLN GLY SER ILE PHE ASP GLY SEQRES 11 A 330 GLU LEU CYS VAL ASP ILE VAL GLU LYS LYS PHE ALA PHE SEQRES 12 A 330 VAL LEU PHE ASP ALA VAL VAL VAL SER GLY VAL THR VAL SEQRES 13 A 330 SER GLN MET ASP LEU ALA SER ARG PHE PHE ALA MET LYS SEQRES 14 A 330 ARG SER LEU LYS GLU PHE LYS ASN VAL PRO GLU ASP PRO SEQRES 15 A 330 ALA ILE LEU ARG TYR LYS GLU TRP ILE PRO LEU GLU HIS SEQRES 16 A 330 PRO THR ILE ILE LYS ASP HIS LEU LYS LYS ALA ASN ALA SEQRES 17 A 330 ILE TYR HIS THR ASP GLY LEU ILE ILE MET SER VAL ASP SEQRES 18 A 330 GLU PRO VAL ILE TYR GLY ARG ASN PHE ASN LEU PHE LYS SEQRES 19 A 330 LEU LYS PRO GLY THR HIS HIS THR ILE ASP PHE ILE ILE SEQRES 20 A 330 MET SER GLU ASP GLY THR ILE GLY ILE PHE ASP PRO ASN SEQRES 21 A 330 LEU ARG LYS ASN VAL PRO VAL GLY LYS LEU ASP GLY TYR SEQRES 22 A 330 TYR ASN LYS GLY SER ILE VAL GLU CYS GLY PHE ALA ASP SEQRES 23 A 330 GLY THR TRP LYS TYR ILE GLN GLY ARG SER ASP LYS ASN SEQRES 24 A 330 GLN ALA ASN ASP ARG LEU THR TYR GLU LYS THR LEU LEU SEQRES 25 A 330 ASN ILE GLU GLU ASN ILE THR ILE ASP GLU LEU LEU ASP SEQRES 26 A 330 LEU PHE LYS TRP GLU SEQRES 1 B 330 MET VAL PRO PRO THR ILE ASN THR GLY LYS ASN ILE THR SEQRES 2 B 330 THR GLU ARG ALA VAL LEU THR LEU ASN GLY LEU GLN ILE SEQRES 3 B 330 LYS LEU HIS LYS VAL VAL GLY GLU SER ARG ASP ASP ILE SEQRES 4 B 330 VAL ALA LYS MET LYS ASP LEU ALA MET ASP ASP HIS LYS SEQRES 5 B 330 PHE PRO ARG LEU PRO GLY PRO ASN PRO VAL SER ILE GLU SEQRES 6 B 330 ARG LYS ASP PHE GLU LYS LEU LYS GLN ASN LYS TYR VAL SEQRES 7 B 330 VAL SER GLU GPL THR ASP GLY ILE ARG PHE MET MET PHE SEQRES 8 B 330 PHE THR ARG VAL PHE GLY PHE LYS VAL CYS THR ILE ILE SEQRES 9 B 330 ASP ARG ALA MET THR VAL TYR LEU LEU PRO PHE LYS ASN SEQRES 10 B 330 ILE PRO ARG VAL LEU PHE GLN GLY SER ILE PHE ASP GLY SEQRES 11 B 330 GLU LEU CYS VAL ASP ILE VAL GLU LYS LYS PHE ALA PHE SEQRES 12 B 330 VAL LEU PHE ASP ALA VAL VAL VAL SER GLY VAL THR VAL SEQRES 13 B 330 SER GLN MET ASP LEU ALA SER ARG PHE PHE ALA MET LYS SEQRES 14 B 330 ARG SER LEU LYS GLU PHE LYS ASN VAL PRO GLU ASP PRO SEQRES 15 B 330 ALA ILE LEU ARG TYR LYS GLU TRP ILE PRO LEU GLU HIS SEQRES 16 B 330 PRO THR ILE ILE LYS ASP HIS LEU LYS LYS ALA ASN ALA SEQRES 17 B 330 ILE TYR HIS THR ASP GLY LEU ILE ILE MET SER VAL ASP SEQRES 18 B 330 GLU PRO VAL ILE TYR GLY ARG ASN PHE ASN LEU PHE LYS SEQRES 19 B 330 LEU LYS PRO GLY THR HIS HIS THR ILE ASP PHE ILE ILE SEQRES 20 B 330 MET SER GLU ASP GLY THR ILE GLY ILE PHE ASP PRO ASN SEQRES 21 B 330 LEU ARG LYS ASN VAL PRO VAL GLY LYS LEU ASP GLY TYR SEQRES 22 B 330 TYR ASN LYS GLY SER ILE VAL GLU CYS GLY PHE ALA ASP SEQRES 23 B 330 GLY THR TRP LYS TYR ILE GLN GLY ARG SER ASP LYS ASN SEQRES 24 B 330 GLN ALA ASN ASP ARG LEU THR TYR GLU LYS THR LEU LEU SEQRES 25 B 330 ASN ILE GLU GLU ASN ILE THR ILE ASP GLU LEU LEU ASP SEQRES 26 B 330 LEU PHE LYS TRP GLU MODRES 1CKN GPL B 82 LYS LYSINE GUANOSINE-5'-MONOPHOSPHATE HET GPL B 82 32 HET GTP A 899 32 HET MN B1001 1 HET SO4 B1000 5 HETNAM GPL LYSINE GUANOSINE-5'-MONOPHOSPHATE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION FORMUL 2 GPL C16 H26 N7 O9 P FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 MN MN 2+ FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *342(H2 O) HELIX 1 1 GLY A 33 LEU A 46 1 14 HELIX 2 2 ARG A 66 GLN A 74 5 9 HELIX 3 3 LEU A 122 GLN A 124 5 3 HELIX 4 4 LEU A 161 SER A 171 1 11 HELIX 5 5 PRO A 196 ILE A 209 1 14 HELIX 6 6 ARG A 304 GLU A 316 1 13 HELIX 7 7 ILE A 320 LEU A 326 1 7 HELIX 8 8 GLY B 33 ALA B 47 5 15 HELIX 9 9 ARG B 66 GLN B 74 5 9 HELIX 10 10 ARG B 120 GLN B 124 5 5 HELIX 11 11 LEU B 161 LEU B 172 1 12 HELIX 12 12 PRO B 196 ALA B 208 1 13 HELIX 13 13 PRO B 259 LEU B 261 5 3 HELIX 14 14 ARG B 304 GLU B 315 1 12 HELIX 15 15 ILE B 320 ASP B 325 1 6 SHEET 1 A 8 THR A 14 LEU A 21 0 SHEET 2 A 8 LEU A 24 VAL A 31 -1 N LYS A 30 O GLU A 15 SHEET 3 A 8 VAL A 110 LEU A 112 -1 N LEU A 112 O HIS A 29 SHEET 4 A 8 PHE A 98 ILE A 104 -1 N ILE A 103 O TYR A 111 SHEET 5 A 8 ILE A 86 VAL A 95 -1 N VAL A 95 O PHE A 98 SHEET 6 A 8 SER A 126 ASP A 135 -1 N LEU A 132 O ILE A 86 SHEET 7 A 8 LYS A 140 LEU A 145 -1 N VAL A 144 O GLU A 131 SHEET 8 A 8 ILE A 184 TYR A 187 1 N ILE A 184 O PHE A 143 SHEET 1 B 3 TYR A 77 GLU A 81 0 SHEET 2 B 3 LEU A 215 SER A 219 -1 N MET A 218 O VAL A 78 SHEET 3 B 3 LEU A 232 LEU A 235 -1 N LEU A 235 O LEU A 215 SHEET 1 C 3 THR A 242 ILE A 246 0 SHEET 2 C 3 ILE A 279 ALA A 285 -1 N CYS A 282 O ILE A 243 SHEET 3 C 3 THR A 288 ARG A 295 -1 N ARG A 295 O ILE A 279 SHEET 1 D 2 GLY A 255 ASP A 258 0 SHEET 2 D 2 LYS A 263 PRO A 266 -1 N VAL A 265 O ILE A 256 SHEET 1 E 2 ILE A 127 ASP A 129 0 SHEET 2 E 2 ASP A 147 VAL A 150 -1 N VAL A 150 O ILE A 127 SHEET 1 F 8 THR B 14 LEU B 21 0 SHEET 2 F 8 LEU B 24 VAL B 31 -1 N LYS B 30 O GLU B 15 SHEET 3 F 8 VAL B 110 LEU B 112 -1 N LEU B 112 O HIS B 29 SHEET 4 F 8 PHE B 98 ASP B 105 -1 N ILE B 103 O TYR B 111 SHEET 5 F 8 ILE B 86 VAL B 95 -1 N VAL B 95 O PHE B 98 SHEET 6 F 8 SER B 126 ASP B 135 -1 N LEU B 132 O ILE B 86 SHEET 7 F 8 LYS B 140 LEU B 145 -1 N VAL B 144 O GLU B 131 SHEET 8 F 8 ILE B 184 TYR B 187 1 N ILE B 184 O PHE B 143 SHEET 1 G 3 TYR B 77 SER B 80 0 SHEET 2 G 3 LEU B 215 SER B 219 -1 N MET B 218 O VAL B 78 SHEET 3 G 3 PHE B 233 LEU B 235 -1 N LEU B 235 O LEU B 215 SHEET 1 H 3 THR B 242 ILE B 246 0 SHEET 2 H 3 ILE B 279 ALA B 285 -1 N CYS B 282 O ILE B 243 SHEET 3 H 3 THR B 288 GLY B 294 -1 N GLN B 293 O GLU B 281 SHEET 1 I 2 ILE B 127 ASP B 129 0 SHEET 2 I 2 ASP B 147 VAL B 150 -1 N VAL B 150 O ILE B 127 SHEET 1 J 2 THR B 253 ASP B 258 0 SHEET 2 J 2 LYS B 263 LYS B 269 -1 N GLY B 268 O ILE B 254 LINK C GLU B 81 N GPL B 82 1555 1555 1.34 LINK C GPL B 82 N THR B 83 1555 1555 1.33 LINK O1P GPL B 82 MN MN B1001 1555 1555 2.40 LINK MN MN B1001 O HOH B1121 1555 1555 2.34 LINK MN MN B1001 O HOH B1122 1555 1555 2.42 LINK MN MN B1001 O HOH B1163 1555 1555 2.33 SITE 1 GMA 1 LYS A 82 SITE 1 GMB 1 GPL B 82 SITE 1 AC1 6 GPL B 82 HOH B1114 HOH B1121 HOH B1122 SITE 2 AC1 6 HOH B1156 HOH B1163 SITE 1 AC2 10 GPL B 82 ARG B 106 ARG B 228 LYS B 234 SITE 2 AC2 10 ASP B 244 LYS B 298 ASN B 302 HOH B1151 SITE 3 AC2 10 HOH B1154 HOH B1171 SITE 1 AC3 19 PRO A 59 PRO A 61 LYS A 82 THR A 83 SITE 2 AC3 19 ARG A 87 ARG A 106 GLU A 131 PHE A 146 SITE 3 AC3 19 LYS A 188 TRP A 190 ILE A 216 LEU A 232 SITE 4 AC3 19 LYS A 234 HOH A 995 HOH A1023 HOH A1032 SITE 5 AC3 19 HOH A1043 HOH A1048 HOH A1050 CRYST1 94.906 212.953 105.016 90.00 90.00 90.00 C 2 2 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 0.010537 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009522 0.00000