PDB Short entry for 1NV8 HEADER TRANSFERASE 02-FEB-03 1NV8 TITLE N5-GLUTAMINE METHYLTRANSFERASE, HEMK COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMK PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: HEMK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODON+; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHIS.PARELLEL3 KEYWDS CLASS I ADOMET-DEPENDENT METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.L.SCHUBERT,J.D.PHILLIPS,C.P.HILL REVDAT 4 14-FEB-24 1NV8 1 REMARK SEQADV LINK REVDAT 3 31-JAN-18 1NV8 1 REMARK REVDAT 2 24-FEB-09 1NV8 1 VERSN REVDAT 1 27-MAY-03 1NV8 0 JRNL AUTH H.L.SCHUBERT,J.D.PHILLIPS,C.P.HILL JRNL TITL STRUCTURES ALONG THE CATALYTIC PATHWAY OF PRMC/HEMK, AN JRNL TITL 2 N(5)-GLUTAMINE ADOMET-DEPENDENT METHYLTRANSFERASE JRNL REF BIOCHEMISTRY V. 42 5592 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12741815 JRNL DOI 10.1021/BI034026P REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 30679 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1646 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1552 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.4770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.260 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.481 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4443 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4203 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5977 ; 2.412 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9781 ; 1.224 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 535 ; 8.645 ; 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): 675 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4806 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 913 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 926 ; 0.232 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4810 ; 0.256 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2754 ; 0.103 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 229 ; 0.236 ; 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): 34 ; 0.279 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 95 ; 0.266 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.403 ; 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): 2683 ; 1.339 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4332 ; 2.435 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1760 ; 3.463 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1645 ; 5.506 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 1NV8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BLU-ICE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 53.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3000, NACITRATE, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 100K 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 70.74450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.53100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.74450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.53100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 -1 REMARK 465 ALA A -2 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 ALA A 10 REMARK 465 GLU A 11 REMARK 465 GLY B -1 REMARK 465 ALA B -2 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 5 REMARK 465 ASN B 6 REMARK 465 VAL B 7 REMARK 465 SER B 8 REMARK 465 GLY B 9 REMARK 465 ALA B 10 REMARK 465 GLU B 11 REMARK 465 ARG B 12 REMARK 465 LYS B 54 REMARK 465 ASP B 55 REMARK 465 SER B 282 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 B 209 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 OD2 ASP B 227 O HOH B 447 2.03 REMARK 500 O PHE B 213 O HOH B 423 2.06 REMARK 500 O HOH A 517 O HOH A 518 2.08 REMARK 500 O HOH B 458 O HOH B 489 2.14 REMARK 500 OH TYR B 200 N MEQ B 401 2.15 REMARK 500 O HOH A 479 O HOH A 491 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 449 O HOH A 526 4555 2.17 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 GLU A 111 CD GLU A 111 OE1 0.073 REMARK 500 GLU A 182 CD GLU A 182 OE1 0.070 REMARK 500 GLU B 192 CD GLU B 192 OE2 -0.096 REMARK 500 MET B 193 SD MET B 193 CE -0.414 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 LEU A 56 CA - CB - CG ANGL. DEV. = 18.6 DEGREES REMARK 500 ARG A 103 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 144 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 193 CG - SD - CE ANGL. DEV. = -10.8 DEGREES REMARK 500 ARG A 273 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 103 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 118 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 172 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG B 176 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 MET B 193 CG - SD - CE ANGL. DEV. = -19.6 DEGREES REMARK 500 ASP B 210 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 250 CB - CG - OD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP B 267 CB - CG - OD2 ANGL. DEV. = 6.8 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 31 65.00 -119.13 REMARK 500 ILE A 46 -168.19 -120.93 REMARK 500 LYS A 48 -44.54 -26.67 REMARK 500 PHE A 180 -125.70 53.87 REMARK 500 GLU A 249 -61.95 -24.20 REMARK 500 ASP A 261 -16.28 87.62 REMARK 500 ALA A 269 6.53 -69.36 REMARK 500 ILE B 14 -56.39 -177.44 REMARK 500 GLU B 26 88.35 -57.90 REMARK 500 PHE B 52 -83.87 -70.99 REMARK 500 SER B 59 139.59 -38.41 REMARK 500 PHE B 180 -119.99 44.98 REMARK 500 LEU B 212 60.38 -108.36 REMARK 500 SER B 260 159.62 -48.50 REMARK 500 ASP B 261 -15.65 87.06 REMARK 500 ASP B 267 -178.18 -23.87 REMARK 500 ALA B 269 22.30 -76.29 REMARK 500 ARG B 273 -15.11 -144.26 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 ASP A 55 LEU A 56 -149.40 REMARK 500 SER A 281 SER A 282 139.71 REMARK 500 PHE B 52 LEU B 53 63.10 REMARK 500 VAL B 211 LEU B 212 144.02 REMARK 500 LEU B 212 PHE B 213 147.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MEQ A 400 REMARK 610 MEQ B 401 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 MEQ B 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAM B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MEQ A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MEQ B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NV9 RELATED DB: PDB REMARK 900 HEMK, APO STRUCTURE DBREF 1NV8 A 1 282 UNP Q9WYV8 Q9WYV8_THEMA 1 282 DBREF 1NV8 B 1 282 UNP Q9WYV8 Q9WYV8_THEMA 1 282 SEQADV 1NV8 GLY A -1 UNP Q9WYV8 EXPRESSION TAG SEQADV 1NV8 ALA A -2 UNP Q9WYV8 EXPRESSION TAG SEQADV 1NV8 GLY B -1 UNP Q9WYV8 EXPRESSION TAG SEQADV 1NV8 ALA B -2 UNP Q9WYV8 EXPRESSION TAG SEQRES 1 A 284 GLY ALA MET ASP THR ARG LYS ASN VAL SER GLY ALA GLU SEQRES 2 A 284 ARG LYS ILE TRP SER LEU ILE ARG ASP CYS SER GLY LYS SEQRES 3 A 284 LEU GLU GLY VAL THR GLU THR SER VAL LEU GLU VAL LEU SEQRES 4 A 284 LEU ILE VAL SER ARG VAL LEU GLY ILE ARG LYS GLU ASP SEQRES 5 A 284 LEU PHE LEU LYS ASP LEU GLY VAL SER PRO THR GLU GLU SEQRES 6 A 284 LYS ARG ILE LEU GLU LEU VAL GLU LYS ARG ALA SER GLY SEQRES 7 A 284 TYR PRO LEU HIS TYR ILE LEU GLY GLU LYS GLU PHE MET SEQRES 8 A 284 GLY LEU SER PHE LEU VAL GLU GLU GLY VAL PHE VAL PRO SEQRES 9 A 284 ARG PRO GLU THR GLU GLU LEU VAL GLU LEU ALA LEU GLU SEQRES 10 A 284 LEU ILE ARG LYS TYR GLY ILE LYS THR VAL ALA ASP ILE SEQRES 11 A 284 GLY THR GLY SER GLY ALA ILE GLY VAL SER VAL ALA LYS SEQRES 12 A 284 PHE SER ASP ALA ILE VAL PHE ALA THR ASP VAL SER SER SEQRES 13 A 284 LYS ALA VAL GLU ILE ALA ARG LYS ASN ALA GLU ARG HIS SEQRES 14 A 284 GLY VAL SER ASP ARG PHE PHE VAL ARG LYS GLY GLU PHE SEQRES 15 A 284 LEU GLU PRO PHE LYS GLU LYS PHE ALA SER ILE GLU MET SEQRES 16 A 284 ILE LEU SER ASN PRO PRO TYR VAL LYS SER SER ALA HIS SEQRES 17 A 284 LEU PRO LYS ASP VAL LEU PHE GLU PRO PRO GLU ALA LEU SEQRES 18 A 284 PHE GLY GLY GLU ASP GLY LEU ASP PHE TYR ARG GLU PHE SEQRES 19 A 284 PHE GLY ARG TYR ASP THR SER GLY LYS ILE VAL LEU MET SEQRES 20 A 284 GLU ILE GLY GLU ASP GLN VAL GLU GLU LEU LYS LYS ILE SEQRES 21 A 284 VAL SER ASP THR VAL PHE LEU LYS ASP SER ALA GLY LYS SEQRES 22 A 284 TYR ARG PHE LEU LEU LEU ASN ARG ARG SER SER SEQRES 1 B 284 GLY ALA MET ASP THR ARG LYS ASN VAL SER GLY ALA GLU SEQRES 2 B 284 ARG LYS ILE TRP SER LEU ILE ARG ASP CYS SER GLY LYS SEQRES 3 B 284 LEU GLU GLY VAL THR GLU THR SER VAL LEU GLU VAL LEU SEQRES 4 B 284 LEU ILE VAL SER ARG VAL LEU GLY ILE ARG LYS GLU ASP SEQRES 5 B 284 LEU PHE LEU LYS ASP LEU GLY VAL SER PRO THR GLU GLU SEQRES 6 B 284 LYS ARG ILE LEU GLU LEU VAL GLU LYS ARG ALA SER GLY SEQRES 7 B 284 TYR PRO LEU HIS TYR ILE LEU GLY GLU LYS GLU PHE MET SEQRES 8 B 284 GLY LEU SER PHE LEU VAL GLU GLU GLY VAL PHE VAL PRO SEQRES 9 B 284 ARG PRO GLU THR GLU GLU LEU VAL GLU LEU ALA LEU GLU SEQRES 10 B 284 LEU ILE ARG LYS TYR GLY ILE LYS THR VAL ALA ASP ILE SEQRES 11 B 284 GLY THR GLY SER GLY ALA ILE GLY VAL SER VAL ALA LYS SEQRES 12 B 284 PHE SER ASP ALA ILE VAL PHE ALA THR ASP VAL SER SER SEQRES 13 B 284 LYS ALA VAL GLU ILE ALA ARG LYS ASN ALA GLU ARG HIS SEQRES 14 B 284 GLY VAL SER ASP ARG PHE PHE VAL ARG LYS GLY GLU PHE SEQRES 15 B 284 LEU GLU PRO PHE LYS GLU LYS PHE ALA SER ILE GLU MET SEQRES 16 B 284 ILE LEU SER ASN PRO PRO TYR VAL LYS SER SER ALA HIS SEQRES 17 B 284 LEU PRO LYS ASP VAL LEU PHE GLU PRO PRO GLU ALA LEU SEQRES 18 B 284 PHE GLY GLY GLU ASP GLY LEU ASP PHE TYR ARG GLU PHE SEQRES 19 B 284 PHE GLY ARG TYR ASP THR SER GLY LYS ILE VAL LEU MET SEQRES 20 B 284 GLU ILE GLY GLU ASP GLN VAL GLU GLU LEU LYS LYS ILE SEQRES 21 B 284 VAL SER ASP THR VAL PHE LEU LYS ASP SER ALA GLY LYS SEQRES 22 B 284 TYR ARG PHE LEU LEU LEU ASN ARG ARG SER SER HET SAM A 300 27 HET MEQ A 400 10 HET SAM B 301 27 HET MEQ B 401 10 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM MEQ N5-METHYLGLUTAMINE FORMUL 3 SAM 2(C15 H22 N6 O5 S) FORMUL 4 MEQ 2(C6 H12 N2 O3) FORMUL 7 HOH *233(H2 O) HELIX 1 1 LYS A 13 LEU A 25 1 13 HELIX 2 2 THR A 31 GLY A 45 1 15 HELIX 3 3 ARG A 47 PHE A 52 5 6 HELIX 4 4 SER A 59 SER A 75 1 17 HELIX 5 5 PRO A 78 GLY A 84 1 7 HELIX 6 6 GLU A 105 GLY A 121 1 17 HELIX 7 7 GLY A 133 SER A 143 1 11 HELIX 8 8 SER A 153 HIS A 167 1 15 HELIX 9 9 LEU A 181 PHE A 188 5 8 HELIX 10 10 LYS A 202 HIS A 206 5 5 HELIX 11 11 PRO A 215 PHE A 220 1 6 HELIX 12 12 LEU A 226 TYR A 236 1 11 HELIX 13 13 GLN A 251 LYS A 256 1 6 HELIX 14 14 ILE B 14 LYS B 24 1 11 HELIX 15 15 THR B 31 GLY B 45 1 15 HELIX 16 16 ARG B 47 PHE B 52 5 6 HELIX 17 17 SER B 59 SER B 75 1 17 HELIX 18 18 PRO B 78 GLY B 84 1 7 HELIX 19 19 PRO B 104 GLY B 121 1 18 HELIX 20 20 GLY B 133 SER B 143 1 11 HELIX 21 21 SER B 153 HIS B 167 1 15 HELIX 22 22 LEU B 181 ILE B 191 5 11 HELIX 23 23 LYS B 209 GLU B 214 5 6 HELIX 24 24 PRO B 215 LEU B 219 5 5 HELIX 25 25 LEU B 226 TYR B 236 1 11 HELIX 26 26 GLN B 251 VAL B 259 1 9 SHEET 1 A 2 GLU A 85 PHE A 88 0 SHEET 2 A 2 LEU A 91 LEU A 94 -1 O LEU A 91 N PHE A 88 SHEET 1 B 7 PHE A 173 LYS A 177 0 SHEET 2 B 7 ILE A 146 ASP A 151 1 N ALA A 149 O PHE A 174 SHEET 3 B 7 THR A 124 ILE A 128 1 N VAL A 125 O ILE A 146 SHEET 4 B 7 MET A 193 SER A 196 1 O LEU A 195 N ALA A 126 SHEET 5 B 7 ILE A 242 GLU A 246 1 O ILE A 242 N ILE A 194 SHEET 6 B 7 TYR A 272 ASN A 278 -1 O LEU A 275 N MET A 245 SHEET 7 B 7 VAL A 263 LYS A 266 -1 N VAL A 263 O LEU A 276 SHEET 1 C 2 GLU B 85 PHE B 88 0 SHEET 2 C 2 LEU B 91 LEU B 94 -1 O PHE B 93 N LYS B 86 SHEET 1 D 7 PHE B 173 LYS B 177 0 SHEET 2 D 7 ILE B 146 ASP B 151 1 N ALA B 149 O PHE B 174 SHEET 3 D 7 THR B 124 ILE B 128 1 N VAL B 125 O ILE B 146 SHEET 4 D 7 MET B 193 SER B 196 1 O MET B 193 N ALA B 126 SHEET 5 D 7 ILE B 242 GLU B 246 1 O ILE B 242 N ILE B 194 SHEET 6 D 7 TYR B 272 ASN B 278 -1 O LEU B 277 N VAL B 243 SHEET 7 D 7 VAL B 263 LYS B 266 -1 N LEU B 265 O PHE B 274 LINK CE SAM A 300 CE MEQ A 400 1555 1555 1.86 SITE 1 AC1 20 PHE A 100 PRO A 102 GLY A 129 THR A 130 SITE 2 AC1 20 GLY A 131 ASP A 151 VAL A 152 GLU A 179 SITE 3 AC1 20 PHE A 180 ASN A 197 PRO A 199 GLU A 217 SITE 4 AC1 20 ALA A 218 MEQ A 400 HOH A 401 HOH A 402 SITE 5 AC1 20 HOH A 404 HOH A 408 HOH A 464 HOH A 467 SITE 1 AC2 21 PHE B 100 PRO B 102 GLY B 129 THR B 130 SITE 2 AC2 21 GLY B 131 ASP B 151 VAL B 152 GLY B 178 SITE 3 AC2 21 GLU B 179 PHE B 180 ASN B 197 PRO B 199 SITE 4 AC2 21 GLU B 217 ALA B 218 MEQ B 401 HOH B 406 SITE 5 AC2 21 HOH B 407 HOH B 409 HOH B 410 HOH B 436 SITE 6 AC2 21 HOH B 488 SITE 1 AC3 9 ARG A 103 ASN A 197 PRO A 198 PRO A 199 SITE 2 AC3 9 TYR A 200 VAL A 201 ALA A 218 LEU A 219 SITE 3 AC3 9 SAM A 300 SITE 1 AC4 6 ASN B 197 PRO B 198 PRO B 199 TYR B 200 SITE 2 AC4 6 LEU B 219 SAM B 301 CRYST1 141.489 59.062 85.605 90.00 109.22 90.00 C 1 2 1 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 0.007068 0.000000 0.002464 0.00000 SCALE2 0.000000 0.016931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012371 0.00000