HEADER TRANSCRIPTION/RNA 18-DEC-07 3BOY TITLE CRYSTAL STRUCTURE OF THE HUTP ANTITERMINATION COMPLEX BOUND TO THE HUT TITLE 2 MRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP*GP*UP*UP*UP*UP*UP*AP COMPND 3 *GP*UP*UP*U)-3'; COMPND 4 CHAIN: D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HUT OPERON POSITIVE REGULATORY PROTEIN; COMPND 8 CHAIN: A, B, C; COMPND 9 SYNONYM: HUTP; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 5 ORGANISM_TAXID: 1423; SOURCE 6 GENE: HUTP; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET5A, PETHP4 KEYWDS HUTP, RNA-BINDING, HUTP-RNA COMPLEX, ANTI-TERMINATION, TRANSCRIPTION KEYWDS 2 REGULATION, ACTIVATOR, HISTIDINE METABOLISM, TRANSCRIPTION-RNA KEYWDS 3 COMPLEX, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 4 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 5 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR T.S.KUMAREVEL,D.BALASUNDARESAN,J.JEYAKANTHAN,A.SHINKAI,S.YOKOYAMA, AUTHOR 2 P.K.R.KUMAR,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 5 01-NOV-23 3BOY 1 REMARK REVDAT 4 10-NOV-21 3BOY 1 REMARK SEQADV LINK REVDAT 3 25-OCT-17 3BOY 1 REMARK REVDAT 2 24-FEB-09 3BOY 1 VERSN REVDAT 1 15-JAN-08 3BOY 0 SPRSDE 15-JAN-08 3BOY 2GZT JRNL AUTH T.KUMAREVEL,D.BALASUNDARESAN,J.JEYAKANTHAN,A.SHINKAI, JRNL AUTH 2 S.YOKOYAMA,P.K.R.KUMAR JRNL TITL CRYSTAL STRUCTURE OF HUTP COMPLEXED WITH THE 55-MER RNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KUMAREVEL,Z.FUJIMOTO,P.KARTHE,M.ODA,H.MIZUNO,P.K.R.KUMAR REMARK 1 TITL CRYSTAL STRUCTURE OF ACTIVATED HUTP: AN RNA BINDING PROTEIN REMARK 1 TITL 2 THAT REGULATES TRANSCRIPTION OF THE HUT OPERON IN BACILLUS REMARK 1 TITL 3 SUBTILIS REMARK 1 REF STRUCTURE V. 12 1269 2004 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 15242603 REMARK 1 DOI 10.1016/J.STR.2004.05.005 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.KUMAREVEL,S.C.B.GOPINATH,S.NISHIKAWA,H.MIZUNO,P.K.R.KUMAR REMARK 1 TITL IDENTIFICATION OF IMPORTANT CHEMICAL GROUPS OF THE HUT MRNA REMARK 1 TITL 2 FOR HUTP INTERACTIONS THAT REGULATE THE HUT OPERON IN REMARK 1 TITL 3 BACILLUS SUBTILIS REMARK 1 REF NUCLEIC ACIDS RES. V. 32 3904 2004 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 15273277 REMARK 1 DOI 10.1093/NAR/GKH725 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.KUMAREVEL,H.MIZUNO,P.K.R.KUMAR REMARK 1 TITL STRUCTURAL BASIS OF HUTP-MEDIATED ANTI-TERMINATION AND ROLES REMARK 1 TITL 2 OF THE MG2+ ION AND L-HISTIDINE LIGAND REMARK 1 REF NATURE V. 434 183 2005 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 15758992 REMARK 1 DOI 10.1038/NATURE03355 REMARK 1 REFERENCE 4 REMARK 1 AUTH T.KUMAREVEL,H.MIZUNO,P.K.R.KUMAR REMARK 1 TITL CHARACTERIZATION OF THE METAL ION BINDING SITE IN THE REMARK 1 TITL 2 ANTI-TERMINATOR PROTEIN, HUTP, OF BACILLUS SUBTILIS REMARK 1 REF NUCLEIC ACIDS RES. V. 33 5494 2005 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 16192572 REMARK 1 DOI 10.1093/NAR/GKI868 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 45893 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2445 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) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3241 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3393 REMARK 3 NUCLEIC ACID ATOMS : 435 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 406 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.627 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3905 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5352 ; 1.560 ; 2.103 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 438 ; 6.087 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;30.533 ;22.950 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 589 ;16.588 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;15.902 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 622 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2743 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1868 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2601 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 306 ; 0.179 ; 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): 144 ; 0.261 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 62 ; 0.246 ; 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): 2231 ; 1.070 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3434 ; 1.652 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1977 ; 2.291 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1918 ; 3.627 ; 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 : 1.20 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 3BOY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI II CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36200 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: 1WMQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD, 0.1M HEPES, 0.1M MGCL2, PH REMARK 280 7.40, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 49.81750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.23450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.81750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.23450 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 29750 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, A, B, C 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 BIOMT1 2 -1.000000 0.000000 0.000000 -20.50458 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 59.34767 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 U D 22 O5' C5' C4' O4' C3' O3' C2' REMARK 470 U D 22 O2' C1' N1 C2 O2 N3 C4 REMARK 470 U D 22 O4 C5 C6 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU A 15 CD1 REMARK 480 LEU A 17 CD2 REMARK 480 THR A 25 CB OG1 CG2 REMARK 480 GLU A 29 CG CD OE1 OE2 REMARK 480 LYS A 36 CD CE NZ REMARK 480 SER A 66 OG REMARK 480 GLU A 67 CG CD OE1 OE2 REMARK 480 ARG A 70 CG NH2 REMARK 480 GLU A 81 OE2 REMARK 480 LEU B 15 CD1 REMARK 480 LEU B 17 CD2 REMARK 480 GLU B 29 CG CD OE1 OE2 REMARK 480 LYS B 36 CD CE NZ REMARK 480 SER B 66 OG REMARK 480 GLU B 67 CG CD OE1 OE2 REMARK 480 GLU B 81 OE2 REMARK 480 LEU C 15 CD1 REMARK 480 LEU C 17 CD2 REMARK 480 THR C 25 CB OG1 CG2 REMARK 480 GLU C 29 CG CD OE1 OE2 REMARK 480 SER C 66 OG REMARK 480 GLU C 67 CG CD OE1 OE2 REMARK 480 ARG C 70 CG NH2 REMARK 480 GLU C 81 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 O2' U D 7 OG1 THR A 56 1.94 REMARK 500 OE2 GLU A 81 O HOH A 3081 2.05 REMARK 500 OE2 GLU B 90 O HOH B 3082 2.18 REMARK 500 OE2 GLU B 67 O HOH B 3042 2.18 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 OE1 GLU A 67 OE2 GLU C 23 3546 0.66 REMARK 500 OE2 GLU A 67 OE1 GLU C 23 3546 1.15 REMARK 500 OE1 GLU A 67 CD GLU C 23 3546 1.25 REMARK 500 NH2 ARG C 70 O ILE C 148 2556 1.50 REMARK 500 CD GLU A 67 OE1 GLU C 23 3546 1.58 REMARK 500 NH2 ARG A 70 OXT ILE B 148 2556 1.60 REMARK 500 OXT ILE A 148 NH1 ARG B 70 2556 1.73 REMARK 500 OE1 GLU A 67 OE1 GLU C 23 3546 1.80 REMARK 500 NH2 ARG B 32 O ARG C 32 1545 1.90 REMARK 500 CD GLU A 67 OE2 GLU C 23 3546 1.91 REMARK 500 CD GLU A 67 CD GLU C 23 3546 1.96 REMARK 500 NZ LYS C 134 O HOH A 3052 2556 2.15 REMARK 500 NH2 ARG B 32 C ARG C 32 1545 2.16 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 ARG A 70 CG ARG A 70 CD 0.459 REMARK 500 ARG A 70 CZ ARG A 70 NH2 0.263 REMARK 500 CYS B 38 CB CYS B 38 SG -0.127 REMARK 500 SER B 66 CB SER B 66 OG -0.167 REMARK 500 GLU B 81 CD GLU B 81 OE2 0.107 REMARK 500 LEU C 17 CG LEU C 17 CD2 -0.337 REMARK 500 GLU C 29 CB GLU C 29 CG -0.185 REMARK 500 CYS C 38 CB CYS C 38 SG -0.117 REMARK 500 ARG C 70 CG ARG C 70 CD 0.312 REMARK 500 ARG C 70 CZ ARG C 70 NH2 0.147 REMARK 500 GLU C 81 CD GLU C 81 OE2 0.227 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 G D 5 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U D 7 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 U D 7 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 G D 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 U D 14 C2 - N1 - C1' ANGL. DEV. = 7.6 DEGREES REMARK 500 U D 14 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 G D 19 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 G D 19 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 70 CB - CG - CD ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG A 70 CG - CD - NE ANGL. DEV. = -34.0 DEGREES REMARK 500 ARG A 70 NH1 - CZ - NH2 ANGL. DEV. = -13.3 DEGREES REMARK 500 GLU B 81 CG - CD - OE2 ANGL. DEV. = -16.5 DEGREES REMARK 500 LEU C 17 CB - CG - CD2 ANGL. DEV. = 25.0 DEGREES REMARK 500 ARG C 70 CG - CD - NE ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG C 70 NE - CZ - NH2 ANGL. DEV. = -15.4 DEGREES REMARK 500 GLU C 81 CG - CD - OE2 ANGL. DEV. = -20.9 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 ALA A 21 108.08 -56.25 REMARK 500 LEU A 93 -89.72 -119.27 REMARK 500 PRO A 132 49.36 -73.26 REMARK 500 GLU B 22 53.30 -111.50 REMARK 500 LEU B 93 -90.45 -116.57 REMARK 500 PRO B 132 48.78 -73.04 REMARK 500 SER C 24 -61.28 -106.54 REMARK 500 LEU C 93 -88.95 -117.87 REMARK 500 PRO C 132 47.13 -73.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 70 0.17 SIDE CHAIN REMARK 500 GLU A 81 0.14 SIDE CHAIN REMARK 500 GLU B 81 0.15 SIDE CHAIN REMARK 500 ARG C 70 0.17 SIDE CHAIN REMARK 500 GLU C 81 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 1001 REMARK 615 HIS A 2001 REMARK 615 HIS A 3001 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 A2002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 73 NE2 REMARK 620 2 HIS A 77 NE2 89.1 REMARK 620 3 HIS A2001 O 165.6 92.6 REMARK 620 4 HIS A2001 N 89.9 89.0 75.9 REMARK 620 5 HIS B 138 NE2 90.3 178.7 88.3 92.1 REMARK 620 6 HOH B3066 O 95.3 88.4 99.0 174.2 90.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 138 NE2 REMARK 620 2 HIS A1001 O 89.7 REMARK 620 3 HIS A1001 N 86.4 75.0 REMARK 620 4 HIS C 73 NE2 89.0 164.4 89.4 REMARK 620 5 HIS C 77 NE2 179.1 91.1 93.5 90.1 REMARK 620 6 HOH C3103 O 92.2 98.2 173.0 97.4 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B3002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A3001 N REMARK 620 2 HIS A3001 O 76.5 REMARK 620 3 HIS B 73 NE2 88.6 165.0 REMARK 620 4 HIS B 77 NE2 95.4 93.9 88.3 REMARK 620 5 HOH B3065 O 171.7 95.6 99.3 87.2 REMARK 620 6 HIS C 138 NE2 85.8 88.5 89.5 177.4 91.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VEA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUTP COMPLEXED WITH L-HISTIDINE ANALOG REMARK 900 RELATED ID: 1WPT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUTP REMARK 900 RELATED ID: 1WMQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUTP-RNA COMPLEX REMARK 900 RELATED ID: 1WPU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUTP BOUND TO THE RNA REMARK 900 RELATED ID: 1WRQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF HUTP (HUTP-L-HISTIDINE- REMARK 900 MG2+) REMARK 900 RELATED ID: 1WPV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUTP COMPLEX REMARK 900 RELATED ID: AR_001000707.1 RELATED DB: TARGETDB DBREF 3BOY A 2 148 UNP P10943 HUTP_BACSU 2 148 DBREF 3BOY B 2 148 UNP P10943 HUTP_BACSU 2 148 DBREF 3BOY C 2 148 UNP P10943 HUTP_BACSU 2 148 DBREF 3BOY D 1 22 PDB 3BOY 3BOY 1 22 SEQADV 3BOY ILE A 51 UNP P10943 VAL 51 ENGINEERED MUTATION SEQADV 3BOY ILE B 51 UNP P10943 VAL 51 ENGINEERED MUTATION SEQADV 3BOY ILE C 51 UNP P10943 VAL 51 ENGINEERED MUTATION SEQRES 1 D 22 U U U A G U U U U U A G U SEQRES 2 D 22 U U U U A G U U U SEQRES 1 A 147 THR LEU HIS LYS GLU ARG ARG ILE GLY ARG LEU SER VAL SEQRES 2 A 147 LEU LEU LEU LEU ASN GLU ALA GLU GLU SER THR GLN VAL SEQRES 3 A 147 GLU GLU LEU GLU ARG ASP GLY TRP LYS VAL CYS LEU GLY SEQRES 4 A 147 LYS VAL GLY SER MET ASP ALA HIS LYS VAL ILE ALA ALA SEQRES 5 A 147 ILE GLU THR ALA SER LYS LYS SER GLY VAL ILE GLN SER SEQRES 6 A 147 GLU GLY TYR ARG GLU SER HIS ALA LEU TYR HIS ALA THR SEQRES 7 A 147 MET GLU ALA LEU HIS GLY VAL THR ARG GLY GLU MET LEU SEQRES 8 A 147 LEU GLY SER LEU LEU ARG THR VAL GLY LEU ARG PHE ALA SEQRES 9 A 147 VAL LEU ARG GLY ASN PRO TYR GLU SER GLU ALA GLU GLY SEQRES 10 A 147 ASP TRP ILE ALA VAL SER LEU TYR GLY THR ILE GLY ALA SEQRES 11 A 147 PRO ILE LYS GLY LEU GLU HIS GLU THR PHE GLY VAL GLY SEQRES 12 A 147 ILE ASN HIS ILE SEQRES 1 B 147 THR LEU HIS LYS GLU ARG ARG ILE GLY ARG LEU SER VAL SEQRES 2 B 147 LEU LEU LEU LEU ASN GLU ALA GLU GLU SER THR GLN VAL SEQRES 3 B 147 GLU GLU LEU GLU ARG ASP GLY TRP LYS VAL CYS LEU GLY SEQRES 4 B 147 LYS VAL GLY SER MET ASP ALA HIS LYS VAL ILE ALA ALA SEQRES 5 B 147 ILE GLU THR ALA SER LYS LYS SER GLY VAL ILE GLN SER SEQRES 6 B 147 GLU GLY TYR ARG GLU SER HIS ALA LEU TYR HIS ALA THR SEQRES 7 B 147 MET GLU ALA LEU HIS GLY VAL THR ARG GLY GLU MET LEU SEQRES 8 B 147 LEU GLY SER LEU LEU ARG THR VAL GLY LEU ARG PHE ALA SEQRES 9 B 147 VAL LEU ARG GLY ASN PRO TYR GLU SER GLU ALA GLU GLY SEQRES 10 B 147 ASP TRP ILE ALA VAL SER LEU TYR GLY THR ILE GLY ALA SEQRES 11 B 147 PRO ILE LYS GLY LEU GLU HIS GLU THR PHE GLY VAL GLY SEQRES 12 B 147 ILE ASN HIS ILE SEQRES 1 C 147 THR LEU HIS LYS GLU ARG ARG ILE GLY ARG LEU SER VAL SEQRES 2 C 147 LEU LEU LEU LEU ASN GLU ALA GLU GLU SER THR GLN VAL SEQRES 3 C 147 GLU GLU LEU GLU ARG ASP GLY TRP LYS VAL CYS LEU GLY SEQRES 4 C 147 LYS VAL GLY SER MET ASP ALA HIS LYS VAL ILE ALA ALA SEQRES 5 C 147 ILE GLU THR ALA SER LYS LYS SER GLY VAL ILE GLN SER SEQRES 6 C 147 GLU GLY TYR ARG GLU SER HIS ALA LEU TYR HIS ALA THR SEQRES 7 C 147 MET GLU ALA LEU HIS GLY VAL THR ARG GLY GLU MET LEU SEQRES 8 C 147 LEU GLY SER LEU LEU ARG THR VAL GLY LEU ARG PHE ALA SEQRES 9 C 147 VAL LEU ARG GLY ASN PRO TYR GLU SER GLU ALA GLU GLY SEQRES 10 C 147 ASP TRP ILE ALA VAL SER LEU TYR GLY THR ILE GLY ALA SEQRES 11 C 147 PRO ILE LYS GLY LEU GLU HIS GLU THR PHE GLY VAL GLY SEQRES 12 C 147 ILE ASN HIS ILE HET MG A2002 1 HET HIS A1001 11 HET HIS A2001 11 HET HIS A3001 11 HET MG B3002 1 HET MG C1002 1 HETNAM MG MAGNESIUM ION HETNAM HIS HISTIDINE FORMUL 5 MG 3(MG 2+) FORMUL 6 HIS 3(C6 H10 N3 O2 1+) FORMUL 11 HOH *406(H2 O) HELIX 1 1 ARG A 8 ASN A 19 1 12 HELIX 2 2 THR A 25 ASP A 33 1 9 HELIX 3 3 ASP A 46 SER A 61 1 16 HELIX 4 4 TYR A 69 ARG A 88 1 20 HELIX 5 5 LEU A 93 LEU A 97 5 5 HELIX 6 6 SER A 114 GLY A 118 5 5 HELIX 7 7 HIS B 4 ARG B 7 5 4 HELIX 8 8 ARG B 8 ASN B 19 1 12 HELIX 9 9 GLU B 22 ASP B 33 1 12 HELIX 10 10 ASP B 46 SER B 61 1 16 HELIX 11 11 TYR B 69 ARG B 88 1 20 HELIX 12 12 LEU B 93 LEU B 97 5 5 HELIX 13 13 SER B 114 GLY B 118 5 5 HELIX 14 14 ARG C 8 ASN C 19 1 12 HELIX 15 15 THR C 25 ASP C 33 1 9 HELIX 16 16 ASP C 46 SER C 61 1 16 HELIX 17 17 TYR C 69 ARG C 88 1 20 HELIX 18 18 LEU C 93 LEU C 97 5 5 HELIX 19 19 SER C 114 GLY C 118 5 5 SHEET 1 A 4 LYS A 36 SER A 44 0 SHEET 2 A 4 THR A 99 GLY A 109 -1 O LEU A 102 N VAL A 42 SHEET 3 A 4 TRP A 120 GLY A 130 -1 O TYR A 126 N ARG A 103 SHEET 4 A 4 GLU A 137 HIS A 147 -1 O ASN A 146 N ILE A 121 SHEET 1 B 4 LYS B 36 SER B 44 0 SHEET 2 B 4 THR B 99 GLY B 109 -1 O LEU B 102 N VAL B 42 SHEET 3 B 4 TRP B 120 GLY B 130 -1 O TYR B 126 N ARG B 103 SHEET 4 B 4 GLU B 137 HIS B 147 -1 O ASN B 146 N ILE B 121 SHEET 1 C 4 LYS C 36 SER C 44 0 SHEET 2 C 4 THR C 99 GLY C 109 -1 O LEU C 102 N VAL C 42 SHEET 3 C 4 TRP C 120 GLY C 130 -1 O TYR C 126 N ARG C 103 SHEET 4 C 4 GLU C 137 HIS C 147 -1 O ASN C 146 N ILE C 121 LINK NE2 HIS A 73 MG MG A2002 1555 1555 2.26 LINK NE2 HIS A 77 MG MG A2002 1555 1555 2.31 LINK NE2 HIS A 138 MG MG C1002 1555 1555 2.20 LINK O HIS A1001 MG MG C1002 1555 1555 2.05 LINK N HIS A1001 MG MG C1002 1555 1555 2.38 LINK O HIS A2001 MG MG A2002 1555 1555 2.06 LINK N HIS A2001 MG MG A2002 1555 1555 2.36 LINK MG MG A2002 NE2 HIS B 138 1555 1555 2.23 LINK MG MG A2002 O HOH B3066 1555 1555 2.08 LINK N HIS A3001 MG MG B3002 1555 1555 2.36 LINK O HIS A3001 MG MG B3002 1555 1555 2.03 LINK NE2 HIS B 73 MG MG B3002 1555 1555 2.20 LINK NE2 HIS B 77 MG MG B3002 1555 1555 2.28 LINK MG MG B3002 O HOH B3065 1555 1555 2.04 LINK MG MG B3002 NE2 HIS C 138 1555 1555 2.22 LINK NE2 HIS C 73 MG MG C1002 1555 1555 2.26 LINK NE2 HIS C 77 MG MG C1002 1555 1555 2.31 LINK MG MG C1002 O HOH C3103 1555 1555 2.08 CRYST1 99.635 76.469 62.790 90.00 109.06 90.00 C 1 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 0.010037 0.000000 0.003467 0.00000 SCALE2 0.000000 0.013077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016850 0.00000