HEADER TRANSFERASE 18-JUN-12 4AY7 TITLE METHYLTRANSFERASE FROM METHANOSARCINA MAZEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCOBALAMIN\: COENZYME M METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CORRINOID COENZYME M METHYLTRANSFERASE MTAA; COMPND 5 EC: 2.1.1.247; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 2209; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-15B KEYWDS TRANSFERASE, TIM BARREL EXPDTA X-RAY DIFFRACTION AUTHOR A.HOEPPNER,F.THOMAS,A.RUEPPEL,R.HENSEL,W.BLANKENFELD,P.BAYER,A.FAUST REVDAT 4 20-DEC-23 4AY7 1 REMARK LINK REVDAT 3 05-NOV-14 4AY7 1 REMARK SEQRES MODRES HET REVDAT 3 2 1 HETNAM HETSYN FORMUL LINK REVDAT 3 3 1 HETATM ANISOU MASTER REVDAT 2 07-NOV-12 4AY7 1 JRNL REVDAT 1 31-OCT-12 4AY7 0 JRNL AUTH A.HOEPPNER,F.THOMAS,A.RUEPPEL,R.HENSEL,W.BLANKENFELDT, JRNL AUTH 2 P.BAYER,A.FAUST JRNL TITL STRUCTURE OF THE CORRINOID:COENZYME M METHYLTRANSFERASE MTAA JRNL TITL 2 FROM METHANOSARCINA MAZEI JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 1549 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 23090404 JRNL DOI 10.1107/S090744491203853X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 83.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 51799 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2759 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3830 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 408 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.63 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.687 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5132 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3457 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6992 ; 1.965 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8587 ; 1.078 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 692 ; 6.030 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;34.226 ;25.349 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 898 ;14.425 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;24.605 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 844 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5660 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 875 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 6 A 500 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3088 -0.1005 5.3874 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: 0.0789 REMARK 3 T33: 0.2822 T12: -0.0040 REMARK 3 T13: -0.0396 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 1.1678 L22: 0.6310 REMARK 3 L33: 0.2542 L12: 0.1022 REMARK 3 L13: 0.2016 L23: -0.0773 REMARK 3 S TENSOR REMARK 3 S11: -0.0048 S12: 0.0362 S13: 0.0054 REMARK 3 S21: 0.0229 S22: 0.0042 S23: 0.0240 REMARK 3 S31: -0.0231 S32: -0.0010 S33: 0.0006 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 500 REMARK 3 ORIGIN FOR THE GROUP (A): 3.2316 -42.1982 19.3348 REMARK 3 T TENSOR REMARK 3 T11: 0.0335 T22: 0.0719 REMARK 3 T33: 0.2630 T12: -0.0005 REMARK 3 T13: -0.0573 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.2286 L22: 0.7019 REMARK 3 L33: 0.2633 L12: -0.1433 REMARK 3 L13: -0.0447 L23: 0.0927 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.0505 S13: -0.0128 REMARK 3 S21: -0.0015 S22: 0.0129 S23: 0.0070 REMARK 3 S31: 0.0219 S32: 0.0069 S33: 0.0000 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 : 1.20 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 4AY7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052916. 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 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54605 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 83.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4AY8 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 0.2 M MGCL2, REMARK 280 30%(W/W) PEG 4000, 2% 1,1,1,3,3,3-HEXAFLUORO-2-PROPANOL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 83.70950 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 MET A 4 REMARK 465 SER A 5 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 MET B 4 REMARK 465 SER B 5 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 6 CG CD OE1 OE2 REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 GLU B 136 CG CD OE1 OE2 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 OE1 GLN B 227 O HOH A 2146 2.07 REMARK 500 O HOH A 2152 O HOH A 2164 2.16 REMARK 500 O HOH A 2042 O HOH A 2082 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 HIS A 103 CG HIS A 103 CD2 0.067 REMARK 500 HIS B 103 CG HIS B 103 CD2 0.065 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 B 73 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP B 173 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 337 NE - CZ - NH1 ANGL. DEV. = 3.7 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 HIS A 64 -54.59 -123.49 REMARK 500 GLU A 70 36.11 -94.09 REMARK 500 PRO A 75 -145.91 -85.09 REMARK 500 SER A 160 143.93 87.21 REMARK 500 ASN A 234 44.27 -86.35 REMARK 500 THR A 291 -53.19 -132.51 REMARK 500 PRO B 75 -142.04 -90.15 REMARK 500 SER B 160 147.27 86.29 REMARK 500 ASN B 234 45.37 -82.21 REMARK 500 THR B 291 -59.02 -135.72 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 A 600 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 88 OE2 REMARK 620 2 ASP A 313 OD1 95.3 REMARK 620 3 HOH A2067 O 78.3 91.3 REMARK 620 4 HOH A2068 O 84.6 161.9 70.8 REMARK 620 5 HOH A2199 O 91.2 104.3 162.0 93.9 REMARK 620 6 HOH A2201 O 158.7 96.4 83.6 78.8 103.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 240 NE2 REMARK 620 2 CYS A 242 SG 107.5 REMARK 620 3 CYS A 319 SG 105.8 123.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 600 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 88 OE2 REMARK 620 2 ASP B 313 OD1 91.7 REMARK 620 3 HOH B2065 O 87.0 161.9 REMARK 620 4 HOH B2182 O 87.4 103.0 95.0 REMARK 620 5 HOH B2184 O 179.0 88.9 92.6 91.7 REMARK 620 6 HOH B2185 O 79.3 86.0 76.0 164.2 101.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 240 NE2 REMARK 620 2 CYS B 242 SG 105.4 REMARK 620 3 GLU B 263 OE2 121.6 99.1 REMARK 620 4 CYS B 319 SG 105.7 122.2 104.1 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 ZN A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AY8 RELATED DB: PDB REMARK 900 SEMET-DERIVATIVE OF A METHYLTRANSFERASE FROM M. MAZEI DBREF 4AY7 A 1 342 UNP Q8PXZ6 Q8PXZ6_METMA 1 342 DBREF 4AY7 B 1 342 UNP Q8PXZ6 Q8PXZ6_METMA 1 342 SEQADV 4AY7 HIS A -5 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS A -4 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS A -3 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS A -2 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS A -1 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS A 0 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B -5 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B -4 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B -3 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B -2 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B -1 UNP Q8PXZ6 EXPRESSION TAG SEQADV 4AY7 HIS B 0 UNP Q8PXZ6 EXPRESSION TAG SEQRES 1 A 348 HIS HIS HIS HIS HIS HIS MET THR ASP MET SER GLU PHE SEQRES 2 A 348 THR LEU LYS THR ARG LEU LEU ALA ALA LEU LYS GLY GLU SEQRES 3 A 348 PRO VAL ASP LYS VAL PRO VAL CYS SER VAL THR GLN THR SEQRES 4 A 348 GLY ILE VAL GLU LEU MET ASP VAL VAL GLY ALA PRO TRP SEQRES 5 A 348 PRO GLU ALA HIS THR ASN PRO GLU LEU MET ALA LYS LEU SEQRES 6 A 348 ALA LEU ALA ASN HIS GLU LEU SER GLY LEU GLU ALA VAL SEQRES 7 A 348 ARG LEU PRO TYR CSD LEU THR VAL LEU VAL GLU ALA MET SEQRES 8 A 348 GLY CYS GLU ILE ASN MET GLY THR LYS ASN ARG GLN PRO SEQRES 9 A 348 SER VAL THR GLY HIS PRO TYR PRO LYS ASP LEU GLU GLY SEQRES 10 A 348 ALA ALA VAL PRO ALA ASP LEU LEU GLN ARG GLY ARG ILE SEQRES 11 A 348 PRO VAL VAL LEU GLU ALA ILE LYS ILE ILE ARG GLU LYS SEQRES 12 A 348 VAL GLY PRO ASP VAL PRO ILE VAL GLY GLY MET GLU GLY SEQRES 13 A 348 PRO VAL THR VAL ALA SER ASP LEU VAL SER VAL LYS SER SEQRES 14 A 348 PHE MET LYS TRP SER ILE LYS LYS THR ASP LEU LEU GLU SEQRES 15 A 348 GLN ALA LEU ASP ILE ALA THR GLU ALA SER ILE ILE TYR SEQRES 16 A 348 ALA ASN ALA MET VAL GLU ALA GLY ALA ASP VAL ILE ALA SEQRES 17 A 348 ILE ALA ASP PRO VAL ALA SER PRO ASP LEU MET SER PRO SEQRES 18 A 348 ASP SER PHE ARG GLN PHE LEU LYS SER ARG LEU GLN LYS SEQRES 19 A 348 PHE ALA SER SER VAL ASN SER VAL THR VAL LEU HIS ILE SEQRES 20 A 348 CYS GLY ASN VAL ASN PRO ILE LEU SER ASP MET ALA ASP SEQRES 21 A 348 CYS GLY PHE GLU GLY LEU SER VAL GLU GLU LYS ILE GLY SEQRES 22 A 348 SER ALA LYS LYS GLY LYS GLU VAL ILE GLY THR ARG ALA SEQRES 23 A 348 ARG LEU VAL GLY ASN VAL SER SER PRO PHE THR LEU LEU SEQRES 24 A 348 PRO GLY PRO VAL ASP LYS ILE LYS ALA GLU ALA LYS GLU SEQRES 25 A 348 ALA LEU GLU GLY GLY ILE ASP VAL LEU ALA PRO GLY CYS SEQRES 26 A 348 GLY ILE ALA PRO MET THR PRO LEU GLU ASN VAL LYS ALA SEQRES 27 A 348 LEU VAL ALA ALA ARG ASP GLU PHE TYR ALA SEQRES 1 B 348 HIS HIS HIS HIS HIS HIS MET THR ASP MET SER GLU PHE SEQRES 2 B 348 THR LEU LYS THR ARG LEU LEU ALA ALA LEU LYS GLY GLU SEQRES 3 B 348 PRO VAL ASP LYS VAL PRO VAL CYS SER VAL THR GLN THR SEQRES 4 B 348 GLY ILE VAL GLU LEU MET ASP VAL VAL GLY ALA PRO TRP SEQRES 5 B 348 PRO GLU ALA HIS THR ASN PRO GLU LEU MET ALA LYS LEU SEQRES 6 B 348 ALA LEU ALA ASN HIS GLU LEU SER GLY LEU GLU ALA VAL SEQRES 7 B 348 ARG LEU PRO TYR CSD LEU THR VAL LEU VAL GLU ALA MET SEQRES 8 B 348 GLY CYS GLU ILE ASN MET GLY THR LYS ASN ARG GLN PRO SEQRES 9 B 348 SER VAL THR GLY HIS PRO TYR PRO LYS ASP LEU GLU GLY SEQRES 10 B 348 ALA ALA VAL PRO ALA ASP LEU LEU GLN ARG GLY ARG ILE SEQRES 11 B 348 PRO VAL VAL LEU GLU ALA ILE LYS ILE ILE ARG GLU LYS SEQRES 12 B 348 VAL GLY PRO ASP VAL PRO ILE VAL GLY GLY MET GLU GLY SEQRES 13 B 348 PRO VAL THR VAL ALA SER ASP LEU VAL SER VAL LYS SER SEQRES 14 B 348 PHE MET LYS TRP SER ILE LYS LYS THR ASP LEU LEU GLU SEQRES 15 B 348 GLN ALA LEU ASP ILE ALA THR GLU ALA SER ILE ILE TYR SEQRES 16 B 348 ALA ASN ALA MET VAL GLU ALA GLY ALA ASP VAL ILE ALA SEQRES 17 B 348 ILE ALA ASP PRO VAL ALA SER PRO ASP LEU MET SER PRO SEQRES 18 B 348 ASP SER PHE ARG GLN PHE LEU LYS SER ARG LEU GLN LYS SEQRES 19 B 348 PHE ALA SER SER VAL ASN SER VAL THR VAL LEU HIS ILE SEQRES 20 B 348 CYS GLY ASN VAL ASN PRO ILE LEU SER ASP MET ALA ASP SEQRES 21 B 348 CYS GLY PHE GLU GLY LEU SER VAL GLU GLU LYS ILE GLY SEQRES 22 B 348 SER ALA LYS LYS GLY LYS GLU VAL ILE GLY THR ARG ALA SEQRES 23 B 348 ARG LEU VAL GLY ASN VAL SER SER PRO PHE THR LEU LEU SEQRES 24 B 348 PRO GLY PRO VAL ASP LYS ILE LYS ALA GLU ALA LYS GLU SEQRES 25 B 348 ALA LEU GLU GLY GLY ILE ASP VAL LEU ALA PRO GLY CYS SEQRES 26 B 348 GLY ILE ALA PRO MET THR PRO LEU GLU ASN VAL LYS ALA SEQRES 27 B 348 LEU VAL ALA ALA ARG ASP GLU PHE TYR ALA MODRES 4AY7 CSD A 77 CYS 3-SULFINOALANINE MODRES 4AY7 CSD B 77 CYS 3-SULFINOALANINE HET CSD A 77 8 HET CSD B 77 8 HET ZN A 500 1 HET MG A 600 1 HET ZN B 500 1 HET MG B 600 1 HETNAM CSD 3-SULFINOALANINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD 2(C3 H7 N O4 S) FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *408(H2 O) HELIX 1 1 THR A 8 GLY A 19 1 12 HELIX 2 2 ILE A 35 GLY A 43 1 9 HELIX 3 3 PRO A 47 ASN A 52 1 6 HELIX 4 4 ASN A 52 LEU A 66 1 15 HELIX 5 5 THR A 79 MET A 85 1 7 HELIX 6 6 ASP A 117 ARG A 121 5 5 HELIX 7 7 ARG A 123 GLY A 139 1 17 HELIX 8 8 GLY A 150 SER A 160 1 11 HELIX 9 9 SER A 160 LYS A 171 1 12 HELIX 10 10 LYS A 171 GLY A 197 1 27 HELIX 11 11 PRO A 206 SER A 209 5 4 HELIX 12 12 SER A 214 VAL A 233 1 20 HELIX 13 13 VAL A 245 ASP A 254 1 10 HELIX 14 14 GLU A 263 GLY A 267 5 5 HELIX 15 15 SER A 268 GLY A 277 1 10 HELIX 16 16 SER A 287 LEU A 293 1 7 HELIX 17 17 PRO A 296 GLY A 310 1 15 HELIX 18 18 PRO A 326 TYR A 341 1 16 HELIX 19 19 THR B 8 GLY B 19 1 12 HELIX 20 20 ILE B 35 GLY B 43 1 9 HELIX 21 21 PRO B 47 ASN B 52 1 6 HELIX 22 22 ASN B 52 LEU B 66 1 15 HELIX 23 23 THR B 79 MET B 85 1 7 HELIX 24 24 ASP B 117 ARG B 121 5 5 HELIX 25 25 ARG B 123 GLY B 139 1 17 HELIX 26 26 GLY B 150 SER B 160 1 11 HELIX 27 27 SER B 160 LYS B 171 1 12 HELIX 28 28 LYS B 171 GLY B 197 1 27 HELIX 29 29 PRO B 206 SER B 209 5 4 HELIX 30 30 SER B 214 LEU B 222 1 9 HELIX 31 31 LEU B 222 VAL B 233 1 12 HELIX 32 32 VAL B 245 ASP B 254 1 10 HELIX 33 33 GLU B 263 GLY B 267 5 5 HELIX 34 34 SER B 268 GLY B 277 1 10 HELIX 35 35 SER B 287 LEU B 293 1 7 HELIX 36 36 PRO B 296 GLY B 310 1 15 HELIX 37 37 PRO B 326 TYR B 341 1 16 SHEET 1 AA 7 VAL A 72 LEU A 74 0 SHEET 2 AA 7 ILE A 144 GLU A 149 1 O VAL A 145 N LEU A 74 SHEET 3 AA 7 VAL A 200 ALA A 204 1 O VAL A 200 N GLY A 146 SHEET 4 AA 7 VAL A 236 HIS A 240 1 O VAL A 236 N ILE A 201 SHEET 5 AA 7 GLY A 259 SER A 261 1 O GLY A 259 N LEU A 239 SHEET 6 AA 7 ARG A 281 VAL A 286 1 O ARG A 281 N LEU A 260 SHEET 7 AA 7 VAL A 314 PRO A 317 1 O VAL A 314 N GLY A 284 SHEET 1 AB 2 GLU A 88 ASN A 90 0 SHEET 2 AB 2 SER A 99 GLY A 102 -1 O SER A 99 N ASN A 90 SHEET 1 BA 7 VAL B 72 LEU B 74 0 SHEET 2 BA 7 ILE B 144 GLU B 149 1 O VAL B 145 N LEU B 74 SHEET 3 BA 7 VAL B 200 ALA B 204 1 O VAL B 200 N GLY B 146 SHEET 4 BA 7 VAL B 236 HIS B 240 1 O VAL B 236 N ILE B 201 SHEET 5 BA 7 GLY B 259 SER B 261 1 O GLY B 259 N LEU B 239 SHEET 6 BA 7 ARG B 281 VAL B 286 1 O ARG B 281 N LEU B 260 SHEET 7 BA 7 VAL B 314 PRO B 317 1 O VAL B 314 N GLY B 284 SHEET 1 BB 2 GLU B 88 ASN B 90 0 SHEET 2 BB 2 SER B 99 GLY B 102 -1 O SER B 99 N ASN B 90 LINK C TYR A 76 N CSD A 77 1555 1555 1.31 LINK C CSD A 77 N LEU A 78 1555 1555 1.33 LINK C TYR B 76 N CSD B 77 1555 1555 1.32 LINK C CSD B 77 N LEU B 78 1555 1555 1.32 LINK OE2 GLU A 88 MG MG A 600 1655 1555 2.23 LINK NE2 HIS A 240 ZN ZN A 500 1555 1555 2.23 LINK SG CYS A 242 ZN ZN A 500 1555 1555 2.41 LINK OD1 ASP A 313 MG MG A 600 1555 1555 2.19 LINK SG CYS A 319 ZN ZN A 500 1555 1555 2.53 LINK MG MG A 600 O HOH A2067 1555 1655 2.39 LINK MG MG A 600 O HOH A2068 1555 1655 2.49 LINK MG MG A 600 O HOH A2199 1555 1555 2.09 LINK MG MG A 600 O HOH A2201 1555 1555 2.03 LINK OE2 GLU B 88 MG MG B 600 1455 1555 2.11 LINK NE2 HIS B 240 ZN ZN B 500 1555 1555 2.25 LINK SG CYS B 242 ZN ZN B 500 1555 1555 2.61 LINK OE2 GLU B 263 ZN ZN B 500 1555 1555 2.50 LINK OD1 ASP B 313 MG MG B 600 1555 1555 2.21 LINK SG CYS B 319 ZN ZN B 500 1555 1555 2.33 LINK MG MG B 600 O HOH B2065 1555 1455 2.24 LINK MG MG B 600 O HOH B2182 1555 1555 2.14 LINK MG MG B 600 O HOH B2184 1555 1555 2.03 LINK MG MG B 600 O HOH B2185 1555 1555 2.23 CISPEP 1 TRP A 46 PRO A 47 0 -0.17 CISPEP 2 LEU A 74 PRO A 75 0 -8.46 CISPEP 3 GLY A 284 ASN A 285 0 -2.73 CISPEP 4 GLY A 295 PRO A 296 0 3.94 CISPEP 5 TRP B 46 PRO B 47 0 0.78 CISPEP 6 LEU B 74 PRO B 75 0 -1.68 CISPEP 7 GLY B 284 ASN B 285 0 -5.90 CISPEP 8 GLY B 295 PRO B 296 0 5.76 SITE 1 AC1 3 HIS A 240 CYS A 242 CYS A 319 SITE 1 AC2 7 GLU A 88 LYS A 273 ASP A 313 HOH A2067 SITE 2 AC2 7 HOH A2068 HOH A2199 HOH A2201 SITE 1 AC3 4 HIS B 240 CYS B 242 GLU B 263 CYS B 319 SITE 1 AC4 6 GLU B 88 ASP B 313 HOH B2065 HOH B2182 SITE 2 AC4 6 HOH B2184 HOH B2185 CRYST1 44.209 167.419 45.849 90.00 117.36 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022620 0.000000 0.011705 0.00000 SCALE2 0.000000 0.005973 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024558 0.00000