HEADER TRANSFERASE 07-JUN-10 3NDJ TITLE X-RAY STRUCTURE OF A C-3'-METHYLTRANSFERASE IN COMPLEX WITH S- TITLE 2 ADENOSYL-L-HOMOCYSTEINE AND SUGAR PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROMONOSPORA CHALCEA; SOURCE 3 ORGANISM_TAXID: 1874; SOURCE 4 GENE: TCAB9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASIMD; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS S-ADENOSYL-L-HOMOCYSTEINE, KIJANOSE, TETRONITROSE, TETRADEOXY SUGAR, KEYWDS 2 KETO SUGAR, MICROMONOSPORA CHALCEA, TCAB9, C-3'-METHYLTRANSFERASE, KEYWDS 3 SUGAR METHYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.BRUENDER,J.B.THODEN,M.KAUR,M.K.AVEY,H.M.HOLDEN REVDAT 5 03-APR-24 3NDJ 1 REMARK REVDAT 4 21-FEB-24 3NDJ 1 REMARK SEQADV LINK REVDAT 3 23-MAY-12 3NDJ 1 HETATM VERSN REVDAT 2 11-AUG-10 3NDJ 1 JRNL REVDAT 1 30-JUN-10 3NDJ 0 JRNL AUTH N.A.BRUENDER,J.B.THODEN,M.KAUR,M.K.AVEY,H.M.HOLDEN JRNL TITL MOLECULAR ARCHITECTURE OF A C-3'-METHYLTRANSFERASE INVOLVED JRNL TITL 2 IN THE BIOSYNTHESIS OF D-TETRONITROSE. JRNL REF BIOCHEMISTRY V. 49 5891 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20527922 JRNL DOI 10.1021/BI100782B REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 66407 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3476 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4681 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 250 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 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) : 10.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : 0.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.060 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.596 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3359 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4582 ; 2.222 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 420 ; 6.212 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;37.236 ;23.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;14.036 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;18.017 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 500 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2622 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2045 ; 1.656 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3298 ; 2.321 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1314 ; 3.493 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1276 ; 4.990 ; 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 : 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: NULL REMARK 4 REMARK 4 3NDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NICKEL FILTER REMARK 200 OPTICS : MONTEL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84778 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 57.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.210 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.42 REMARK 200 R MERGE FOR SHELL (I) : 0.25400 REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: IN-HOUSE MIR MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M - 1.5 M SODIUM/POTASSIUM REMARK 280 PHOSPHATE, 10 MM DTMP, 5 MM S-ADENOSYL-L-HOMOCYSTEINE. , PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 50.47200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.22350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.47200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.22350 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 580 LIES ON A SPECIAL POSITION. 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 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 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 O HOH A 527 O HOH A 799 1.95 REMARK 500 OD2 ASP A 288 O HOH A 654 2.01 REMARK 500 O HOH A 619 O HOH A 682 2.06 REMARK 500 O HOH A 441 O HOH A 751 2.10 REMARK 500 O HOH A 585 O HOH A 587 2.14 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 OG1 THR A 269 OD1 ASN A 355 3555 2.06 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 48 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 199 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 223 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 LEU A 228 CB - CG - CD1 ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP A 247 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 264 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR A 378 CB - CG - CD2 ANGL. DEV. = -4.1 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 LEU A 41 134.44 -37.36 REMARK 500 HIS A 73 -166.15 -173.33 REMARK 500 THR A 100 -73.86 -122.67 REMARK 500 ASP A 106 67.85 -153.51 REMARK 500 ASN A 115 -133.34 48.96 REMARK 500 THR A 178 -43.82 -136.47 REMARK 500 HIS A 362 32.94 72.38 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 ZN A 416 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 13 SG REMARK 620 2 CYS A 16 SG 115.0 REMARK 620 3 CYS A 54 SG 105.0 98.2 REMARK 620 4 CYS A 57 SG 105.9 121.1 110.3 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 SAH A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE JHZ A 418 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NDI RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH S-ADENOSYLMETHIONINE AND DTMP DBREF 3NDJ A 1 414 UNP B5L6K6 B5L6K6_MICCH 1 414 SEQADV 3NDJ GLY A -1 UNP B5L6K6 EXPRESSION TAG SEQADV 3NDJ HIS A 0 UNP B5L6K6 EXPRESSION TAG SEQRES 1 A 416 GLY HIS MET SER HIS LEU ALA ASP VAL SER PRO PRO THR SEQRES 2 A 416 ALA CYS ARG VAL CYS GLY GLY GLY VAL GLN GLU PHE LEU SEQRES 3 A 416 ASP LEU GLY ARG GLN PRO LEU SER ASP ARG PHE ARG LYS SEQRES 4 A 416 PRO ASP GLU LEU ASP ASP GLU PHE THR TYR ARG LEU ALA SEQRES 5 A 416 VAL GLY ARG CYS ASP SER CYS GLU MET VAL GLN LEU THR SEQRES 6 A 416 GLU GLU VAL PRO ARG ASP LEU MET PHE HIS GLU VAL TYR SEQRES 7 A 416 PRO TYR HIS SER SER GLY SER SER VAL MET ARG GLU HIS SEQRES 8 A 416 PHE ALA MET LEU ALA ARG ASP PHE LEU ALA THR GLU LEU SEQRES 9 A 416 THR GLY PRO ASP PRO PHE ILE VAL GLU ILE GLY CYS ASN SEQRES 10 A 416 ASP GLY ILE MET LEU ARG THR ILE GLN GLU ALA GLY VAL SEQRES 11 A 416 ARG HIS LEU GLY PHE GLU PRO SER SER GLY VAL ALA ALA SEQRES 12 A 416 LYS ALA ARG GLU LYS GLY ILE ARG VAL ARG THR ASP PHE SEQRES 13 A 416 PHE GLU LYS ALA THR ALA ASP ASP VAL ARG ARG THR GLU SEQRES 14 A 416 GLY PRO ALA ASN VAL ILE TYR ALA ALA ASN THR LEU CYS SEQRES 15 A 416 HIS ILE PRO TYR VAL GLN SER VAL LEU GLU GLY VAL ASP SEQRES 16 A 416 ALA LEU LEU ALA PRO ASP GLY VAL PHE VAL PHE GLU ASP SEQRES 17 A 416 PRO TYR LEU GLY ASP ILE VAL ALA LYS THR SER PHE ASP SEQRES 18 A 416 GLN ILE TYR ASP GLU HIS PHE PHE LEU PHE SER ALA THR SEQRES 19 A 416 SER VAL GLN GLY MET ALA GLN ARG CYS GLY PHE GLU LEU SEQRES 20 A 416 VAL ASP VAL GLN ARG LEU PRO VAL HIS GLY GLY GLU VAL SEQRES 21 A 416 ARG TYR THR LEU ALA ARG GLN GLY SER ARG THR PRO SER SEQRES 22 A 416 ALA ALA VAL ALA GLN LEU LEU ALA ALA GLU ARG GLU GLN SEQRES 23 A 416 GLU LEU SER ASP MET ALA THR LEU ARG ALA PHE ALA GLY SEQRES 24 A 416 ASN VAL VAL LYS ILE ARG ASP GLU LEU THR ALA LEU LEU SEQRES 25 A 416 HIS ARG LEU ARG ALA GLU GLY ARG SER VAL VAL GLY TYR SEQRES 26 A 416 GLY ALA THR ALA LYS SER ALA THR VAL THR ASN PHE CYS SEQRES 27 A 416 GLY ILE GLY PRO ASP LEU VAL HIS SER VAL TYR ASP THR SEQRES 28 A 416 THR PRO ASP LYS GLN ASN ARG LEU THR PRO GLY ALA HIS SEQRES 29 A 416 ILE PRO VAL ARG PRO ALA SER ALA PHE SER ASP PRO TYR SEQRES 30 A 416 PRO ASP TYR ALA LEU LEU PHE ALA TRP ASN HIS ALA GLU SEQRES 31 A 416 GLU ILE MET ALA LYS GLU GLN GLU PHE HIS GLN ALA GLY SEQRES 32 A 416 GLY ARG TRP ILE LEU TYR VAL PRO GLU VAL HIS ILE ARG HET SAH A 415 26 HET ZN A 416 1 HET PO4 A 417 5 HET JHZ A 418 35 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION HETNAM JHZ (2R,4S,6R)-4-AMINO-4,6-DIMETHYL-5-OXOTETRAHYDRO-2H- HETNAM 2 JHZ PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4- HETNAM 3 JHZ DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2- HETNAM 4 JHZ YL]METHYL DIHYDROGEN DIPHOSPHATE (NON-PREFERRED NAME) FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 ZN ZN 2+ FORMUL 4 PO4 O4 P 3- FORMUL 5 JHZ C17 H27 N3 O13 P2 FORMUL 6 HOH *408(H2 O) HELIX 1 1 PRO A 67 PHE A 72 1 6 HELIX 2 2 HIS A 79 GLY A 82 5 4 HELIX 3 3 SER A 83 THR A 100 1 18 HELIX 4 4 MET A 119 ALA A 126 1 8 HELIX 5 5 SER A 136 GLU A 145 1 10 HELIX 6 6 GLU A 156 GLY A 168 1 13 HELIX 7 7 THR A 178 ILE A 182 5 5 HELIX 8 8 TYR A 184 LEU A 195 1 12 HELIX 9 9 TYR A 208 THR A 216 1 9 HELIX 10 10 SER A 217 ILE A 221 5 5 HELIX 11 11 SER A 230 ARG A 240 1 11 HELIX 12 12 PRO A 252 GLY A 255 5 4 HELIX 13 13 SER A 271 GLN A 284 1 14 HELIX 14 14 ASP A 288 GLU A 316 1 29 HELIX 15 15 LYS A 328 GLY A 337 1 10 HELIX 16 16 THR A 350 GLN A 354 5 5 HELIX 17 17 SER A 369 PHE A 371 5 3 HELIX 18 18 ALA A 383 ASN A 385 5 3 HELIX 19 19 HIS A 386 GLU A 394 1 9 HELIX 20 20 GLU A 394 ALA A 400 1 7 SHEET 1 A 4 VAL A 20 PRO A 30 0 SHEET 2 A 4 THR A 46 CYS A 54 -1 O VAL A 51 N PHE A 23 SHEET 3 A 4 VAL A 60 LEU A 62 -1 O GLN A 61 N GLY A 52 SHEET 4 A 4 PHE A 227 LEU A 228 -1 O LEU A 228 N VAL A 60 SHEET 1 B 7 VAL A 150 ARG A 151 0 SHEET 2 B 7 ARG A 129 PHE A 133 1 N GLY A 132 O ARG A 151 SHEET 3 B 7 PHE A 108 ILE A 112 1 N GLU A 111 O PHE A 133 SHEET 4 B 7 ALA A 170 ALA A 176 1 O TYR A 174 N ILE A 112 SHEET 5 B 7 LEU A 196 PRO A 207 1 O ALA A 197 N ALA A 170 SHEET 6 B 7 GLU A 257 ARG A 264 -1 O LEU A 262 N PHE A 202 SHEET 7 B 7 PHE A 243 LEU A 251 -1 N GLN A 249 O ARG A 259 SHEET 1 C 7 ARG A 356 LEU A 357 0 SHEET 2 C 7 PRO A 364 PRO A 367 -1 O VAL A 365 N ARG A 356 SHEET 3 C 7 VAL A 346 ASP A 348 1 N VAL A 346 O ARG A 366 SHEET 4 C 7 VAL A 320 TYR A 323 1 N GLY A 322 O TYR A 347 SHEET 5 C 7 TYR A 378 LEU A 381 1 O LEU A 380 N VAL A 321 SHEET 6 C 7 ARG A 403 LEU A 406 1 O ILE A 405 N LEU A 381 SHEET 7 C 7 HIS A 412 ILE A 413 -1 O HIS A 412 N LEU A 406 LINK SG CYS A 13 ZN ZN A 416 1555 1555 2.37 LINK SG CYS A 16 ZN ZN A 416 1555 1555 2.31 LINK SG CYS A 54 ZN ZN A 416 1555 1555 2.37 LINK SG CYS A 57 ZN ZN A 416 1555 1555 2.27 CISPEP 1 ASP A 373 PRO A 374 0 1.62 CISPEP 2 VAL A 408 PRO A 409 0 3.98 SITE 1 AC1 23 PHE A 72 TYR A 76 SER A 80 PHE A 90 SITE 2 AC1 23 ILE A 112 GLY A 113 ASN A 115 PHE A 133 SITE 3 AC1 23 GLU A 134 PRO A 135 SER A 136 PHE A 154 SITE 4 AC1 23 PHE A 155 ALA A 176 ASN A 177 THR A 178 SITE 5 AC1 23 ILE A 182 TYR A 184 JHZ A 418 HOH A 454 SITE 6 AC1 23 HOH A 499 HOH A 505 HOH A 512 SITE 1 AC2 4 CYS A 13 CYS A 16 CYS A 54 CYS A 57 SITE 1 AC3 4 PRO A 67 ARG A 68 HOH A 455 HOH A 514 SITE 1 AC4 26 TYR A 76 TYR A 78 ASN A 177 HIS A 181 SITE 2 AC4 26 TYR A 222 GLU A 224 HIS A 225 HIS A 254 SITE 3 AC4 26 GLY A 324 THR A 326 ALA A 327 LYS A 328 SITE 4 AC4 26 ASP A 348 THR A 349 THR A 350 LYS A 353 SITE 5 AC4 26 ASN A 385 HIS A 386 GLU A 389 ILE A 390 SITE 6 AC4 26 LYS A 393 SAH A 415 HOH A 461 HOH A 468 SITE 7 AC4 26 HOH A 479 HOH A 504 CRYST1 100.944 114.447 37.825 90.00 90.00 90.00 P 21 21 2 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 0.009906 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026438 0.00000