HEADER RNA BINDING PROTEIN/RNA 14-MAY-18 5ZW4 TITLE CRYSTAL STRUCTURE OF TRNA BOUND TRMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE O-METHYLTRANSFERASE YRRM; COMPND 3 CHAIN: A; COMPND 4 EC: 2.1.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'- COMPND 8 R(*CP*CP*UP*GP*CP*UP*UP*UP*GP*CP*AP*CP*GP*CP*AP*GP*G)-3'); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: YRRM, BSU27360; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 12 ORGANISM_TAXID: 224308 KEYWDS TRANSFERASE, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.KIM,H.RYU,S.C.ALMO REVDAT 4 22-NOV-23 5ZW4 1 COMPND REVDAT 3 10-OCT-18 5ZW4 1 COMPND JRNL REVDAT 2 25-JUL-18 5ZW4 1 JRNL REVDAT 1 11-JUL-18 5ZW4 0 JRNL AUTH H.RYU,T.L.GROVE,S.C.ALMO,J.KIM JRNL TITL IDENTIFICATION OF A NOVEL TRNA WOBBLE URIDINE MODIFYING JRNL TITL 2 ACTIVITY IN THE BIOSYNTHESIS OF 5-METHOXYURIDINE. JRNL REF NUCLEIC ACIDS RES. V. 46 9160 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29982645 JRNL DOI 10.1093/NAR/GKY592 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 30082 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1613 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1986 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2950 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1755 REMARK 3 NUCLEIC ACID ATOMS : 317 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.25000 REMARK 3 B12 (A**2) : 0.04000 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.243 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2223 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 1904 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3076 ; 2.003 ; 1.859 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4434 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 295 ; 7.561 ; 6.254 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;36.947 ;24.022 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;17.420 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;24.105 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 340 ; 0.160 ; 0.202 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2223 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 450 ; 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 2 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): -28.1146 6.8175 -30.1587 REMARK 3 T TENSOR REMARK 3 T11: 0.1176 T22: 0.0606 REMARK 3 T33: 0.0237 T12: 0.0078 REMARK 3 T13: -0.0024 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.2775 L22: 0.1327 REMARK 3 L33: 0.4820 L12: -0.1211 REMARK 3 L13: -0.0681 L23: -0.0626 REMARK 3 S TENSOR REMARK 3 S11: 0.0077 S12: -0.0591 S13: -0.0073 REMARK 3 S21: -0.0077 S22: -0.0113 S23: 0.0362 REMARK 3 S31: -0.0958 S32: 0.0843 S33: 0.0036 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 : D 27 D 43 REMARK 3 ORIGIN FOR THE GROUP (A): -9.9777 8.5676 -10.0517 REMARK 3 T TENSOR REMARK 3 T11: 0.1885 T22: 0.2178 REMARK 3 T33: 0.3709 T12: -0.0422 REMARK 3 T13: 0.2186 T23: -0.0510 REMARK 3 L TENSOR REMARK 3 L11: 6.9325 L22: 3.6279 REMARK 3 L33: 13.4046 L12: -4.0478 REMARK 3 L13: 6.3201 L23: -5.2039 REMARK 3 S TENSOR REMARK 3 S11: 0.6415 S12: -0.7718 S13: 0.1712 REMARK 3 S21: -0.1355 S22: 0.8255 S23: 0.0761 REMARK 3 S31: -0.4008 S32: -0.8049 S33: -1.4671 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5ZW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300006430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32851 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.80500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 2GPY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M AMMONIUM PHOSPHATE MONOBASIC, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 84.45333 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 42.22667 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 42.22667 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 84.45333 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: 910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 MET A 1 REMARK 465 GLY A 218 REMARK 465 HIS A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 HIS A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 GLY A 225 REMARK 465 A D 37 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 32 CG CD OE1 OE2 REMARK 470 C D 36 O5' C5' C4' O4' C3' O3' C2' REMARK 470 C D 36 O2' C1' N1 C2 O2 N3 C4 REMARK 470 C D 36 N4 C5 C6 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 OP2 C D 36 OP2 C D 36 6554 1.75 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 MET A 43 CG - SD - CE ANGL. DEV. = -19.6 DEGREES REMARK 500 ASP A 113 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 34 43.96 39.76 REMARK 500 ALA A 64 -121.94 48.24 REMARK 500 ALA A 135 87.04 33.84 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 PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 302 DBREF 5ZW4 A 1 217 UNP O32036 YRRM_BACSU 1 217 DBREF 5ZW4 D 27 43 PDB 5ZW4 5ZW4 27 43 SEQADV 5ZW4 GLY A 218 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 219 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 220 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 221 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 222 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 223 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 HIS A 224 UNP O32036 EXPRESSION TAG SEQADV 5ZW4 GLY A 225 UNP O32036 EXPRESSION TAG SEQRES 1 A 225 MET THR ASP ARG TYR GLU GLN ILE ASN ASP TYR ILE GLU SEQRES 2 A 225 ALA LEU LEU LYS PRO ARG PRO ASP ASN VAL LYS ARG LEU SEQRES 3 A 225 GLU ALA TYR ALA GLU GLU HIS HIS VAL PRO ILE MET GLU SEQRES 4 A 225 LYS ALA GLY MET GLU VAL LEU LEU GLN ILE LEU SER VAL SEQRES 5 A 225 LYS GLN PRO LYS LYS ILE LEU GLU ILE GLY THR ALA ILE SEQRES 6 A 225 GLY TYR SER ALA ILE ARG MET ALA LEU GLU LEU PRO SER SEQRES 7 A 225 ALA GLU ILE TYR THR ILE GLU ARG ASN GLU LYS ARG HIS SEQRES 8 A 225 GLU GLU ALA VAL ASN ASN ILE LYS GLU PHE GLN LEU ASP SEQRES 9 A 225 ASP ARG ILE HIS VAL PHE TYR GLY ASP ALA LEU GLU LEU SEQRES 10 A 225 ALA ASP ALA VAL HIS VAL THR ALA PRO TYR ASP VAL ILE SEQRES 11 A 225 PHE ILE ASP ALA ALA LYS GLY GLN TYR GLN ASN PHE PHE SEQRES 12 A 225 HIS LEU TYR GLU PRO MET LEU SER PRO ASP GLY VAL ILE SEQRES 13 A 225 ILE THR ASP ASN VAL LEU PHE LYS GLY LEU VAL ALA GLU SEQRES 14 A 225 ASP TYR SER LYS ILE GLU PRO LYS ARG ARG ARG ARG LEU SEQRES 15 A 225 VAL ALA LYS ILE ASP GLU TYR ASN HIS TRP LEU MET ASN SEQRES 16 A 225 HIS PRO ASP TYR GLN THR ALA ILE ILE PRO VAL GLY ASP SEQRES 17 A 225 GLY LEU ALA ILE SER LYS LYS LYS ARG GLY HIS HIS HIS SEQRES 18 A 225 HIS HIS HIS GLY SEQRES 1 D 17 C C U G C U U U G C A C G SEQRES 2 D 17 C A G G HET PO4 A 301 5 HET SAM A 302 27 HETNAM PO4 PHOSPHATE ION HETNAM SAM S-ADENOSYLMETHIONINE FORMUL 3 PO4 O4 P 3- FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 5 HOH *162(H2 O) HELIX 1 AA1 ASP A 3 LEU A 16 1 14 HELIX 2 AA2 PRO A 20 HIS A 33 1 14 HELIX 3 AA3 GLU A 39 GLN A 54 1 16 HELIX 4 AA4 GLY A 66 LEU A 76 1 11 HELIX 5 AA5 ASN A 87 PHE A 101 1 15 HELIX 6 AA6 ASP A 113 GLU A 116 5 4 HELIX 7 AA7 LEU A 117 VAL A 123 1 7 HELIX 8 AA8 ALA A 135 GLY A 137 5 3 HELIX 9 AA9 GLN A 138 GLU A 147 1 10 HELIX 10 AB1 LEU A 162 GLU A 169 5 8 HELIX 11 AB2 PRO A 176 HIS A 196 1 21 SHEET 1 AA1 7 ILE A 107 TYR A 111 0 SHEET 2 AA1 7 GLU A 80 GLU A 85 1 N THR A 83 O PHE A 110 SHEET 3 AA1 7 LYS A 57 ILE A 61 1 N GLU A 60 O TYR A 82 SHEET 4 AA1 7 TYR A 127 ILE A 132 1 O PHE A 131 N LEU A 59 SHEET 5 AA1 7 LEU A 150 ASP A 159 1 O ILE A 157 N ILE A 132 SHEET 6 AA1 7 LEU A 210 LYS A 215 -1 O SER A 213 N ILE A 156 SHEET 7 AA1 7 TYR A 199 ILE A 204 -1 N ILE A 204 O LEU A 210 CISPEP 1 ALA A 125 PRO A 126 0 4.48 CISPEP 2 GLU A 175 PRO A 176 0 -10.89 SITE 1 AC1 7 ASP A 104 ILE A 107 HIS A 108 VAL A 109 SITE 2 AC1 7 HIS A 144 TRP A 192 HOH A 433 SITE 1 AC2 21 ILE A 37 MET A 38 GLU A 60 GLY A 62 SITE 2 AC2 21 THR A 63 ALA A 64 TYR A 67 SER A 68 SITE 3 AC2 21 GLU A 85 ARG A 86 ARG A 90 GLY A 112 SITE 4 AC2 21 ASP A 113 ALA A 114 ASP A 133 ALA A 134 SITE 5 AC2 21 ALA A 135 PHE A 142 HOH A 406 HOH A 474 SITE 6 AC2 21 HOH A 480 CRYST1 64.982 64.982 126.680 90.00 90.00 120.00 P 32 2 1 6 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 0.015389 0.008885 0.000000 0.00000 SCALE2 0.000000 0.017770 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007894 0.00000