HEADER OXIDOREDUCTASE 04-SEP-08 3EE4 TITLE R2-LIKE LIGAND BINDING MN/FE OXIDASE FROM M. TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MN/FE LIGAND BINDING OXIDASE; COMPND 5 EC: 1.17.4.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: NRDB, RV0233; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCR-T7 KEYWDS MANGANESE, IRON, DIIRON, CARBOXYLATE, OXIDASE, R2, LIGAND, CAVITY, KEYWDS 2 MONOOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.S.ANDERSSON,T.A.JONES,M.HOGBOM REVDAT 3 13-JUL-11 3EE4 1 VERSN REVDAT 2 21-APR-09 3EE4 1 JRNL REVDAT 1 07-APR-09 3EE4 0 JRNL AUTH C.S.ANDERSSON JRNL TITL A MYCOBACTERIUM TUBERCULOSIS LIGAND-BINDING MN/FE PROTEIN JRNL TITL 2 REVEALS A NEW COFACTOR IN A REMODELED R2-PROTEIN SCAFFOLD JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 5633 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19321420 JRNL DOI 10.1073/PNAS.0812971106 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0073 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23650 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1727 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2319 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -0.63000 REMARK 3 B12 (A**2) : 0.21000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.545 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2392 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1658 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3236 ; 1.699 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3977 ; 1.410 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 288 ; 5.194 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 125 ;32.857 ;22.880 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 384 ;13.291 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;18.855 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2698 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 540 ; 0.002 ; 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): 1438 ; 1.024 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 583 ; 0.324 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2298 ; 1.872 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 954 ; 3.311 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 938 ; 5.263 ; 4.500 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 : 1 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 290 REMARK 3 ORIGIN FOR THE GROUP (A): 26.8030 19.5440 8.2990 REMARK 3 T TENSOR REMARK 3 T11: -0.0707 T22: -0.0443 REMARK 3 T33: -0.0341 T12: 0.0142 REMARK 3 T13: 0.0065 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.9943 L22: 0.6082 REMARK 3 L33: 1.7824 L12: -0.1017 REMARK 3 L13: 0.2712 L23: -0.0681 REMARK 3 S TENSOR REMARK 3 S11: 0.0054 S12: 0.0324 S13: 0.0136 REMARK 3 S21: 0.0521 S22: 0.0146 S23: -0.0851 REMARK 3 S31: 0.0029 S32: 0.1909 S33: -0.0200 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3EE4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-08. REMARK 100 THE RCSB ID CODE IS RCSB049208. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24918 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36200 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 180MM CALCIUM ACETATE, 15-18% REMARK 280 PEG18000, 0.1M SODIUM CACODYLATE, PH6.8, VAPOR DIFFUSION, SITTING REMARK 280 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 117.76733 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 58.88367 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 58.88367 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 117.76733 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: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 -8 REMARK 465 ALA A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ASP A 291 REMARK 465 TYR A 292 REMARK 465 SER A 293 REMARK 465 PRO A 294 REMARK 465 ALA A 295 REMARK 465 GLN A 296 REMARK 465 LEU A 297 REMARK 465 GLU A 298 REMARK 465 ASP A 299 REMARK 465 THR A 300 REMARK 465 PHE A 301 REMARK 465 ALA A 302 REMARK 465 ASP A 303 REMARK 465 GLU A 304 REMARK 465 ASP A 305 REMARK 465 ARG A 306 REMARK 465 ARG A 307 REMARK 465 THR A 308 REMARK 465 LEU A 309 REMARK 465 ALA A 310 REMARK 465 ALA A 311 REMARK 465 ALA A 312 REMARK 465 SER A 313 REMARK 465 ALA A 314 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 326 O HOH A 467 1.89 REMARK 500 OE1 GLU A 91 O HOH A 456 1.92 REMARK 500 O HOH A 404 O HOH A 460 2.09 REMARK 500 O HOH A 385 O HOH A 582 2.09 REMARK 500 O HOH A 447 O HOH A 583 2.12 REMARK 500 OE1 GLU A 184 O HOH A 462 2.13 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 O HOH A 402 O HOH A 579 4555 1.65 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 GLU A 167 CG GLU A 167 CD 0.099 REMARK 500 GLU A 167 CD GLU A 167 OE1 0.080 REMARK 500 ARG A 203 CG ARG A 203 CD 0.160 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 132 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU A 194 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 128 71.15 -119.73 REMARK 500 ALA A 137 -67.84 -128.90 REMARK 500 ILE A 165 -62.25 -97.91 REMARK 500 ASP A 220 113.58 -166.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 504 DISTANCE = 5.03 ANGSTROMS REMARK 525 HOH A 570 DISTANCE = 5.08 ANGSTROMS 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 MN3 A 316 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 68 OE1 REMARK 620 2 GLU A 101 OE1 91.0 REMARK 620 3 MYR A 315 O2 81.0 103.0 REMARK 620 4 HOH A 343 O 169.4 90.1 88.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 317 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 101 OE2 REMARK 620 2 GLU A 167 OE2 102.1 REMARK 620 3 GLU A 202 OE1 161.9 95.5 REMARK 620 4 HIS A 205 ND1 86.9 99.1 86.0 REMARK 620 5 MYR A 315 O1 89.5 86.2 96.0 174.2 REMARK 620 6 HOH A 343 O 96.4 161.2 66.4 85.0 90.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MYR A 315 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN3 A 316 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 317 DBREF 3EE4 A 1 314 UNP P96416 P96416_MYCTU 1 314 SEQADV 3EE4 MET A -8 UNP P96416 EXPRESSION TAG SEQADV 3EE4 ALA A -7 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -6 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -5 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -4 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -3 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -2 UNP P96416 EXPRESSION TAG SEQADV 3EE4 HIS A -1 UNP P96416 EXPRESSION TAG SEQADV 3EE4 GLY A 0 UNP P96416 EXPRESSION TAG SEQRES 1 A 323 MET ALA HIS HIS HIS HIS HIS HIS GLY MET THR ARG THR SEQRES 2 A 323 ARG SER GLY SER LEU ALA ALA GLY GLY LEU ASN TRP ALA SEQRES 3 A 323 SER LEU PRO LEU LYS LEU PHE ALA GLY GLY ASN ALA LYS SEQRES 4 A 323 PHE TRP HIS PRO ALA ASP ILE ASP PHE THR ARG ASP ARG SEQRES 5 A 323 ALA ASP TRP GLU LYS LEU SER ASP ASP GLU ARG ASP TYR SEQRES 6 A 323 ALA THR ARG LEU CYS THR GLN PHE ILE ALA GLY GLU GLU SEQRES 7 A 323 ALA VAL THR GLU ASP ILE GLN PRO PHE MET SER ALA MET SEQRES 8 A 323 ARG ALA GLU GLY ARG LEU ALA ASP GLU MET TYR LEU THR SEQRES 9 A 323 GLN PHE ALA PHE GLU GLU ALA LYS HIS THR GLN VAL PHE SEQRES 10 A 323 ARG MET TRP LEU ASP ALA VAL GLY ILE SER GLU ASP LEU SEQRES 11 A 323 HIS ARG TYR LEU ASP ASP LEU PRO ALA TYR ARG GLN ILE SEQRES 12 A 323 PHE TYR ALA GLU LEU PRO GLU CYS LEU ASN ALA LEU SER SEQRES 13 A 323 ALA ASP PRO SER PRO ALA ALA GLN VAL ARG ALA SER VAL SEQRES 14 A 323 THR TYR ASN HIS ILE VAL GLU GLY MET LEU ALA LEU THR SEQRES 15 A 323 GLY TYR TYR ALA TRP HIS LYS ILE CYS VAL GLU ARG ALA SEQRES 16 A 323 ILE LEU PRO GLY MET GLN GLU LEU VAL ARG ARG ILE GLY SEQRES 17 A 323 ASP ASP GLU ARG ARG HIS MET ALA TRP GLY THR PHE THR SEQRES 18 A 323 CYS ARG ARG HIS VAL ALA ALA ASP ASP ALA ASN TRP THR SEQRES 19 A 323 VAL PHE GLU THR ARG MET ASN GLU LEU ILE PRO LEU ALA SEQRES 20 A 323 LEU ARG LEU ILE GLU GLU GLY PHE ALA LEU TYR GLY ASP SEQRES 21 A 323 GLN PRO PRO PHE ASP LEU SER LYS ASP ASP PHE LEU GLN SEQRES 22 A 323 TYR SER THR ASP LYS GLY MET ARG ARG PHE GLY THR ILE SEQRES 23 A 323 SER ASN ALA ARG GLY ARG PRO VAL ALA GLU ILE ASP VAL SEQRES 24 A 323 ASP TYR SER PRO ALA GLN LEU GLU ASP THR PHE ALA ASP SEQRES 25 A 323 GLU ASP ARG ARG THR LEU ALA ALA ALA SER ALA HET MYR A 315 16 HET MN3 A 316 1 HET FE A 317 1 HETNAM MYR MYRISTIC ACID HETNAM MN3 MANGANESE (III) ION HETNAM FE FE (III) ION FORMUL 2 MYR C14 H28 O2 FORMUL 3 MN3 MN 3+ FORMUL 4 FE FE 3+ FORMUL 5 HOH *267(H2 O) HELIX 1 1 SER A 6 ALA A 10 5 5 HELIX 2 2 SER A 18 LYS A 30 1 13 HELIX 3 3 HIS A 33 ILE A 37 5 5 HELIX 4 4 ARG A 41 LEU A 49 1 9 HELIX 5 5 SER A 50 ILE A 75 1 26 HELIX 6 6 ILE A 75 GLU A 85 1 11 HELIX 7 7 ARG A 87 GLY A 116 1 30 HELIX 8 8 LEU A 121 ASP A 126 5 6 HELIX 9 9 LEU A 128 ALA A 137 1 10 HELIX 10 10 ALA A 137 ASP A 149 1 13 HELIX 11 11 SER A 151 ASN A 163 1 13 HELIX 12 12 MET A 169 VAL A 183 1 15 HELIX 13 13 LEU A 188 ASP A 220 1 33 HELIX 14 14 ASP A 221 LEU A 248 1 28 HELIX 15 15 SER A 258 ASN A 279 1 22 HELIX 16 16 PRO A 284 ILE A 288 5 5 LINK OE1 GLU A 68 MN MN3 A 316 1555 1555 2.03 LINK OE1 GLU A 101 MN MN3 A 316 1555 1555 2.00 LINK OE2 GLU A 101 FE FE A 317 1555 1555 2.06 LINK OE2 GLU A 167 FE FE A 317 1555 1555 2.04 LINK OE1 GLU A 202 FE FE A 317 1555 1555 1.93 LINK ND1 HIS A 205 FE FE A 317 1555 1555 2.34 LINK O1 MYR A 315 FE FE A 317 1555 1555 2.18 LINK O2 MYR A 315 MN MN3 A 316 1555 1555 2.04 LINK MN MN3 A 316 O HOH A 343 1555 1555 2.22 LINK FE FE A 317 O HOH A 343 1555 1555 2.14 LINK CB VAL A 71 OH TYR A 162 1555 1555 1.57 SITE 1 AC1 12 TYR A 56 GLU A 68 GLU A 101 VAL A 166 SITE 2 AC1 12 GLU A 167 GLU A 202 PHE A 246 PHE A 262 SITE 3 AC1 12 MN3 A 316 FE A 317 HOH A 343 HOH A 483 SITE 1 AC2 7 GLU A 68 GLU A 101 HIS A 104 MYR A 315 SITE 2 AC2 7 FE A 317 HOH A 343 HOH A 483 SITE 1 AC3 7 GLU A 101 GLU A 167 GLU A 202 HIS A 205 SITE 2 AC3 7 MYR A 315 MN3 A 316 HOH A 343 CRYST1 54.565 54.565 176.651 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 0.018327 0.010581 0.000000 0.00000 SCALE2 0.000000 0.021162 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005661 0.00000