HEADER TRANSFERASE 26-MAY-16 5B6E TITLE CRYSTAL STRUCTURE OF CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE MILA WITH TITLE 2 HMCMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMP 5-HYDROXYMETHYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 5-329; COMPND 5 SYNONYM: CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RIMOFACIENS; SOURCE 3 ORGANISM_TAXID: 504097; SOURCE 4 GENE: MILA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS HYDROXYMETHYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.GONG,G.WU,X.HE REVDAT 2 08-NOV-23 5B6E 1 REMARK REVDAT 1 25-JAN-17 5B6E 0 JRNL AUTH G.ZHAO,C.CHEN,W.XIONG,T.GAO,Z.DENG,G.WU,X.HE JRNL TITL STRUCTURAL BASIS OF THE SUBSTRATE PREFERENCE TOWARDS CMP FOR JRNL TITL 2 A THYMIDYLATE SYNTHASE MILA INVOLVED IN MILDIOMYCIN JRNL TITL 3 BIOSYNTHESIS JRNL REF SCI REP V. 6 39675 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 28000775 JRNL DOI 10.1038/SREP39675 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 68810 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3515 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) : 5043 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 249 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.10000 REMARK 3 B33 (A**2) : 0.34000 REMARK 3 B12 (A**2) : -0.10000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5279 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4881 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7189 ; 0.984 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11109 ; 0.698 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 633 ; 5.085 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 277 ;30.368 ;21.913 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 769 ;11.636 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 63 ;13.717 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 755 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6079 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1398 ; 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): 2546 ; 0.603 ; 1.883 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2547 ; 0.603 ; 1.883 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3173 ; 1.036 ; 2.819 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 5 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6605 70.1768 125.0072 REMARK 3 T TENSOR REMARK 3 T11: 0.0337 T22: 0.0083 REMARK 3 T33: 0.0194 T12: -0.0149 REMARK 3 T13: -0.0068 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.2575 L22: 0.2772 REMARK 3 L33: 0.1189 L12: -0.1458 REMARK 3 L13: 0.0045 L23: -0.0346 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: 0.0149 S13: 0.0206 REMARK 3 S21: -0.0247 S22: 0.0083 S23: 0.0130 REMARK 3 S31: -0.0257 S32: 0.0147 S33: -0.0138 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 5 B 329 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5251 38.6504 132.1501 REMARK 3 T TENSOR REMARK 3 T11: 0.0321 T22: 0.0175 REMARK 3 T33: 0.0154 T12: 0.0029 REMARK 3 T13: 0.0102 T23: 0.0065 REMARK 3 L TENSOR REMARK 3 L11: 0.2971 L22: 0.5034 REMARK 3 L33: 0.0466 L12: -0.2172 REMARK 3 L13: 0.0395 L23: -0.1344 REMARK 3 S TENSOR REMARK 3 S11: -0.0218 S12: -0.0250 S13: -0.0592 REMARK 3 S21: -0.0415 S22: 0.0206 S23: 0.0255 REMARK 3 S31: 0.0206 S32: 0.0071 S33: 0.0012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5B6E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-14 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68810 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000 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) : 1.86 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5JNH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE TRIHYDRATE(PH REMARK 280 6.5), 1.4 M SODIUM ACETATE TRIHYDRATE, PH 8.5, EVAPORATION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.24467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.62233 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.62233 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.24467 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 THR A 233 REMARK 465 PRO A 234 REMARK 465 ASP A 235 REMARK 465 GLY A 236 REMARK 465 GLY A 237 REMARK 465 PRO A 238 REMARK 465 THR B 233 REMARK 465 PRO B 234 REMARK 465 ASP B 235 REMARK 465 GLY B 236 REMARK 465 GLY B 237 REMARK 465 PRO B 238 REMARK 465 ARG B 239 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 NH1 ARG B 256 O ASP B 280 2.01 REMARK 500 NH2 ARG A 239 O HOH A 501 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 NH2 ARG A 97 NH1 ARG B 18 3565 2.01 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 ARG A 97 -40.10 -130.30 REMARK 500 ARG A 100 -81.47 -115.32 REMARK 500 ARG A 110 66.76 -157.11 REMARK 500 ARG A 181 -68.46 -97.53 REMARK 500 ARG B 100 -85.36 -114.98 REMARK 500 ARG B 110 61.45 -155.14 REMARK 500 ARG B 181 -75.91 -90.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 239 -13.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5HM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5HM B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B6D RELATED DB: PDB DBREF 5B6E A 5 329 UNP B4Y380 B4Y380_9ACTN 5 329 DBREF 5B6E B 5 329 UNP B4Y380 B4Y380_9ACTN 5 329 SEQRES 1 A 325 THR PHE GLY THR PHE GLN ASP ALA TYR LEU SER GLN LEU SEQRES 2 A 325 ARG ASP ILE TYR HIS SER PRO GLU PHE ARG ASN ALA PRO SEQRES 3 A 325 ARG GLY GLN ALA SER ARG GLU ARG ILE GLY ALA GLY PHE SEQRES 4 A 325 ARG LEU LEU ASP PRO VAL GLN ARG HIS ILE SER VAL PRO SEQRES 5 A 325 ALA ARG ARG ALA ASN VAL VAL PHE ASN PHE ALA GLU ALA SEQRES 6 A 325 LEU TRP TYR LEU SER GLY SER ASP ARG LEU ASP PHE ILE SEQRES 7 A 325 GLN TYR TYR ALA PRO GLY ILE ALA ALA TYR SER ALA ASP SEQRES 8 A 325 GLY ARG THR LEU ARG GLY THR ALA TYR GLY PRO ARG ILE SEQRES 9 A 325 PHE ARG HIS PRO ALA GLY GLY VAL ASN GLN TRP GLU ASN SEQRES 10 A 325 VAL VAL LYS THR LEU THR ASP ASP PRO ASP SER LYS ARG SEQRES 11 A 325 ALA VAL ILE GLN ILE PHE ASP PRO ARG GLU LEU ALA VAL SEQRES 12 A 325 ALA ASP ASN ILE ASP VAL ALA CYS THR LEU ALA LEU GLN SEQRES 13 A 325 PHE LEU ILE ARG ASP GLY LEU LEU CYS GLY ILE GLY TYR SEQRES 14 A 325 MET ARG ALA ASN ASP ALA PHE ARG GLY ALA VAL SER ASP SEQRES 15 A 325 VAL PHE SER PHE THR PHE LEU GLN GLU PHE THR ALA ARG SEQRES 16 A 325 TYR LEU GLY LEU GLY ILE GLY THR TYR HIS HIS VAL VAL SEQRES 17 A 325 GLY SER VAL HIS ILE TYR ASP SER ASP ALA ARG TRP ALA SEQRES 18 A 325 GLU ARG VAL LEU ASP ALA ALA THR PRO ASP GLY GLY PRO SEQRES 19 A 325 ARG PRO GLY PHE PRO ALA MET PRO ASP GLY ASP ASN TRP SEQRES 20 A 325 PRO HIS VAL ARG ARG VAL LEU GLU TRP GLU GLU ARG LEU SEQRES 21 A 325 ARG THR ASN ALA ALA ARG LEU SER ALA ASP ALA LEU ASP SEQRES 22 A 325 ALA LEU ASP LEU PRO ALA TYR TRP LYS HIS VAL VAL ALA SEQRES 23 A 325 LEU PHE GLU ALA HIS ARG GLN VAL ARG HIS GLU ASP THR SEQRES 24 A 325 PRO ASP ARG ALA LEU LEU ALA ALA LEU PRO GLU VAL TYR SEQRES 25 A 325 ARG GLN SER LEU ALA VAL LYS TRP PRO GLY HIS PHE GLY SEQRES 1 B 325 THR PHE GLY THR PHE GLN ASP ALA TYR LEU SER GLN LEU SEQRES 2 B 325 ARG ASP ILE TYR HIS SER PRO GLU PHE ARG ASN ALA PRO SEQRES 3 B 325 ARG GLY GLN ALA SER ARG GLU ARG ILE GLY ALA GLY PHE SEQRES 4 B 325 ARG LEU LEU ASP PRO VAL GLN ARG HIS ILE SER VAL PRO SEQRES 5 B 325 ALA ARG ARG ALA ASN VAL VAL PHE ASN PHE ALA GLU ALA SEQRES 6 B 325 LEU TRP TYR LEU SER GLY SER ASP ARG LEU ASP PHE ILE SEQRES 7 B 325 GLN TYR TYR ALA PRO GLY ILE ALA ALA TYR SER ALA ASP SEQRES 8 B 325 GLY ARG THR LEU ARG GLY THR ALA TYR GLY PRO ARG ILE SEQRES 9 B 325 PHE ARG HIS PRO ALA GLY GLY VAL ASN GLN TRP GLU ASN SEQRES 10 B 325 VAL VAL LYS THR LEU THR ASP ASP PRO ASP SER LYS ARG SEQRES 11 B 325 ALA VAL ILE GLN ILE PHE ASP PRO ARG GLU LEU ALA VAL SEQRES 12 B 325 ALA ASP ASN ILE ASP VAL ALA CYS THR LEU ALA LEU GLN SEQRES 13 B 325 PHE LEU ILE ARG ASP GLY LEU LEU CYS GLY ILE GLY TYR SEQRES 14 B 325 MET ARG ALA ASN ASP ALA PHE ARG GLY ALA VAL SER ASP SEQRES 15 B 325 VAL PHE SER PHE THR PHE LEU GLN GLU PHE THR ALA ARG SEQRES 16 B 325 TYR LEU GLY LEU GLY ILE GLY THR TYR HIS HIS VAL VAL SEQRES 17 B 325 GLY SER VAL HIS ILE TYR ASP SER ASP ALA ARG TRP ALA SEQRES 18 B 325 GLU ARG VAL LEU ASP ALA ALA THR PRO ASP GLY GLY PRO SEQRES 19 B 325 ARG PRO GLY PHE PRO ALA MET PRO ASP GLY ASP ASN TRP SEQRES 20 B 325 PRO HIS VAL ARG ARG VAL LEU GLU TRP GLU GLU ARG LEU SEQRES 21 B 325 ARG THR ASN ALA ALA ARG LEU SER ALA ASP ALA LEU ASP SEQRES 22 B 325 ALA LEU ASP LEU PRO ALA TYR TRP LYS HIS VAL VAL ALA SEQRES 23 B 325 LEU PHE GLU ALA HIS ARG GLN VAL ARG HIS GLU ASP THR SEQRES 24 B 325 PRO ASP ARG ALA LEU LEU ALA ALA LEU PRO GLU VAL TYR SEQRES 25 B 325 ARG GLN SER LEU ALA VAL LYS TRP PRO GLY HIS PHE GLY HET 5HM A 401 23 HET 5HM B 401 23 HETNAM 5HM 5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN PHOSPHATE) HETSYN 5HM 5-HYDROXYMETHYLCYTIDINE 5'-MONOPHOSPHATE FORMUL 3 5HM 2(C10 H16 N3 O9 P) FORMUL 5 HOH *201(H2 O) HELIX 1 AA1 THR A 8 SER A 23 1 16 HELIX 2 AA2 ALA A 29 GLN A 33 5 5 HELIX 3 AA3 VAL A 55 ARG A 59 5 5 HELIX 4 AA4 ASN A 61 SER A 74 1 14 HELIX 5 AA5 ARG A 78 TYR A 84 1 7 HELIX 6 AA6 ALA A 86 SER A 93 5 8 HELIX 7 AA7 ALA A 103 ARG A 110 1 8 HELIX 8 AA8 ASN A 117 ASP A 129 1 13 HELIX 9 AA9 ARG A 143 VAL A 147 5 5 HELIX 10 AB1 ARG A 181 GLY A 202 1 22 HELIX 11 AB2 ASP A 221 ALA A 232 1 12 HELIX 12 AB3 ASN A 250 THR A 266 1 17 HELIX 13 AB4 SER A 272 ALA A 278 1 7 HELIX 14 AB5 PRO A 282 HIS A 300 1 19 HELIX 15 AB6 ASP A 305 LEU A 312 1 8 HELIX 16 AB7 PRO A 313 TRP A 324 1 12 HELIX 17 AB8 TRP A 324 GLY A 329 1 6 HELIX 18 AB9 THR B 8 SER B 23 1 16 HELIX 19 AC1 ALA B 29 GLN B 33 5 5 HELIX 20 AC2 VAL B 55 ARG B 59 5 5 HELIX 21 AC3 ASN B 61 SER B 74 1 14 HELIX 22 AC4 ARG B 78 TYR B 84 1 7 HELIX 23 AC5 ALA B 86 SER B 93 5 8 HELIX 24 AC6 ALA B 103 ARG B 110 1 8 HELIX 25 AC7 ASN B 117 ASP B 129 1 13 HELIX 26 AC8 ASP B 141 ALA B 146 5 6 HELIX 27 AC9 ARG B 181 GLY B 202 1 22 HELIX 28 AD1 ASP B 221 ALA B 231 1 11 HELIX 29 AD2 ASN B 250 THR B 266 1 17 HELIX 30 AD3 SER B 272 ALA B 278 1 7 HELIX 31 AD4 PRO B 282 HIS B 300 1 19 HELIX 32 AD5 ASP B 305 LEU B 312 1 8 HELIX 33 AD6 PRO B 313 TRP B 324 1 12 HELIX 34 AD7 TRP B 324 GLY B 329 1 6 SHEET 1 AA1 6 PHE A 26 ASN A 28 0 SHEET 2 AA1 6 SER A 35 LEU A 45 -1 O SER A 35 N ASN A 28 SHEET 3 AA1 6 GLY A 204 TYR A 218 -1 O HIS A 210 N PHE A 43 SHEET 4 AA1 6 LEU A 167 ASP A 178 1 N GLY A 170 O HIS A 209 SHEET 5 AA1 6 THR A 156 ARG A 164 -1 N LEU A 162 O CYS A 169 SHEET 6 AA1 6 VAL A 136 GLN A 138 -1 N ILE A 137 O LEU A 159 SHEET 1 AA2 6 PHE B 26 ASN B 28 0 SHEET 2 AA2 6 SER B 35 LEU B 45 -1 O SER B 35 N ASN B 28 SHEET 3 AA2 6 GLY B 204 TYR B 218 -1 O TYR B 208 N LEU B 45 SHEET 4 AA2 6 LEU B 167 ASP B 178 1 N GLY B 172 O HIS B 209 SHEET 5 AA2 6 THR B 156 ARG B 164 -1 N LEU B 162 O CYS B 169 SHEET 6 AA2 6 VAL B 136 GLN B 138 -1 N ILE B 137 O LEU B 159 SITE 1 AC1 17 ARG A 31 THR A 102 TYR A 104 CYS A 155 SITE 2 AC1 17 ARG A 175 ALA A 176 ASN A 177 ASP A 178 SITE 3 AC1 17 ASP A 186 HIS A 216 TYR A 218 HOH A 508 SITE 4 AC1 17 HOH A 548 HOH A 557 LYS B 133 ARG B 134 SITE 5 AC1 17 HOH B 550 SITE 1 AC2 18 LYS A 133 ARG A 134 ARG B 31 THR B 102 SITE 2 AC2 18 TYR B 104 CYS B 155 ARG B 175 ALA B 176 SITE 3 AC2 18 ASN B 177 ASP B 178 ASP B 186 HIS B 216 SITE 4 AC2 18 TYR B 218 HOH B 508 HOH B 516 HOH B 534 SITE 5 AC2 18 HOH B 560 HOH B 580 CRYST1 109.323 109.323 112.867 90.00 90.00 120.00 P 32 2 1 12 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 0.009147 0.005281 0.000000 0.00000 SCALE2 0.000000 0.010562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008860 0.00000