HEADER DNA BINDING PROTEIN 05-JUL-24 9FZF TITLE TRANSCRIPTIONAL REPRESSOR NRDR FROM E. COLI, ADP/DATP BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REPRESSOR NRDR; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: NRDR, YBAD, B0413, JW0403; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RIBONUCLEOTIDE REDUCTASE, TRANSCRIPTIONAL REPRESSOR, ATP-CONE DOMAIN, KEYWDS 2 ZN-RIBBON DOMAIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.BIMAI,I.ROZMAN GRINBERG,B.M.SJOBERG,D.T.LOGAN REVDAT 2 02-JUL-25 9FZF 1 JRNL REVDAT 1 19-MAR-25 9FZF 0 JRNL AUTH I.ROZMAN GRINBERG,O.BIMAI,S.SHAHID,L.PHILIPP, JRNL AUTH 2 M.MARTINEZ-CARRANZA,I.BANERJEE,D.LUNDIN,P.STENMARK, JRNL AUTH 3 B.M.SJOBERG,D.T.LOGAN JRNL TITL BACTERIAL TRANSCRIPTIONAL REPRESSOR NRDR - A FLEXIBLE JRNL TITL 2 MULTIFACTORIAL NUCLEOTIDE SENSOR. JRNL REF FEBS J. V. 292 3091 2025 JRNL REFN ISSN 1742-464X JRNL PMID 40029022 JRNL DOI 10.1111/FEBS.70037 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.8 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 127.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 49.6 REMARK 3 NUMBER OF REFLECTIONS : 10312 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) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 494 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 9.10 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2723 REMARK 3 BIN FREE R VALUE : 0.3244 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 11 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2404 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.37560 REMARK 3 B22 (A**2) : 3.37560 REMARK 3 B33 (A**2) : -6.75110 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.360 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.458 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.897 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.795 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 2558 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 3452 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 980 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 442 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 2558 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 322 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2106 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.85 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.76 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.14 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 94.2246 -14.8104 29.8501 REMARK 3 T TENSOR REMARK 3 T11: -0.0364 T22: -0.0705 REMARK 3 T33: -0.3897 T12: 0.2693 REMARK 3 T13: 0.1086 T23: -0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.7521 L22: 4.615 REMARK 3 L33: 6.3823 L12: 0.4756 REMARK 3 L13: 0.8193 L23: 4.0234 REMARK 3 S TENSOR REMARK 3 S11: 0.0548 S12: 0.1916 S13: 0.3258 REMARK 3 S21: 0.1916 S22: -0.0944 S23: 0.4474 REMARK 3 S31: 0.3258 S32: 0.4474 S33: 0.0396 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 70.1451 -8.953 26.4595 REMARK 3 T TENSOR REMARK 3 T11: 0.1485 T22: -0.2552 REMARK 3 T33: -0.1894 T12: -0.0443 REMARK 3 T13: 0.0044 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 1.8558 L22: 1.715 REMARK 3 L33: 5.7767 L12: 0.2014 REMARK 3 L13: -1.1447 L23: -0.365 REMARK 3 S TENSOR REMARK 3 S11: -0.051 S12: 0.2282 S13: 0.5019 REMARK 3 S21: 0.2282 S22: 0.0156 S23: -0.3817 REMARK 3 S31: 0.5019 S32: -0.3817 S33: 0.0354 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9FZF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292139779. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC 15-MAR-2019 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10132 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.444 REMARK 200 RESOLUTION RANGE LOW (A) : 127.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 39.10 REMARK 200 R MERGE (I) : 0.31000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : 41.20 REMARK 200 R MERGE FOR SHELL (I) : 2.63500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 0.2 M AMMONIUM REMARK 280 ACETATE, 45% (V/V) MPD, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 57.20333 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 28.60167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.20333 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 28.60167 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.20333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 28.60167 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 57.20333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 28.60167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 73.56300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -127.41485 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.60167 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 147.12600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 85.80500 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 147.12600 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 85.80500 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 LYS A 150 REMARK 465 LEU A 151 REMARK 465 ALA A 152 REMARK 465 ALA A 153 REMARK 465 ALA A 154 REMARK 465 LEU A 155 REMARK 465 GLU A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 LYS B 150 REMARK 465 LEU B 151 REMARK 465 ALA B 152 REMARK 465 ALA B 153 REMARK 465 ALA B 154 REMARK 465 LEU B 155 REMARK 465 GLU B 156 REMARK 465 HIS B 157 REMARK 465 HIS B 158 REMARK 465 HIS B 159 REMARK 465 HIS B 160 REMARK 465 HIS B 161 REMARK 465 HIS B 162 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 B 322 O HOH B 369 4655 2.15 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 PHE A 7 31.38 100.37 REMARK 500 LEU A 74 34.06 -94.27 REMARK 500 SER A 133 81.44 55.75 REMARK 500 CYS B 6 -61.85 -93.71 REMARK 500 PHE B 7 -9.98 153.65 REMARK 500 ASP B 15 142.83 173.63 REMARK 500 ARG B 17 141.53 -171.72 REMARK 500 LEU B 74 33.76 -93.84 REMARK 500 SER B 133 82.80 42.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 CYS A 6 SG 111.3 REMARK 620 3 CYS A 31 SG 110.0 100.4 REMARK 620 4 CYS A 34 SG 111.3 108.7 114.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DTP A 200 O2G REMARK 620 2 DTP A 200 O2B 96.2 REMARK 620 3 DTP A 200 O2A 105.8 98.7 REMARK 620 4 ADP A 201 O3B 87.4 82.9 166.4 REMARK 620 5 ADP A 201 O2A 166.2 97.2 75.1 91.3 REMARK 620 6 HOH A 301 O 67.6 156.0 102.6 78.9 98.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 3 SG REMARK 620 2 CYS B 6 SG 120.0 REMARK 620 3 CYS B 31 SG 103.7 101.1 REMARK 620 4 CYS B 34 SG 109.1 115.0 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DTP B 200 O3G REMARK 620 2 DTP B 200 O2B 97.3 REMARK 620 3 DTP B 200 O2A 113.4 94.8 REMARK 620 4 ADP B 201 O1B 82.3 101.1 156.1 REMARK 620 5 ADP B 201 O2A 163.5 96.5 74.4 86.1 REMARK 620 6 HOH B 302 O 82.3 179.0 86.2 77.9 83.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FVR RELATED DB: PDB REMARK 900 RELATED ID: 9FXK RELATED DB: PDB REMARK 900 RELATED ID: EMD-50819 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-50849 RELATED DB: EMDB DBREF 9FZF A 1 149 UNP P0A8D0 NRDR_ECOLI 1 149 DBREF 9FZF B 1 149 UNP P0A8D0 NRDR_ECOLI 1 149 SEQADV 9FZF ASP A 139 UNP P0A8D0 GLU 139 CONFLICT SEQADV 9FZF LYS A 150 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF LEU A 151 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA A 152 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA A 153 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA A 154 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF LEU A 155 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF GLU A 156 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 157 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 158 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 159 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 160 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 161 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS A 162 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ASP B 139 UNP P0A8D0 GLU 139 CONFLICT SEQADV 9FZF LYS B 150 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF LEU B 151 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA B 152 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA B 153 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF ALA B 154 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF LEU B 155 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF GLU B 156 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 157 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 158 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 159 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 160 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 161 UNP P0A8D0 EXPRESSION TAG SEQADV 9FZF HIS B 162 UNP P0A8D0 EXPRESSION TAG SEQRES 1 A 162 MET HIS CYS PRO PHE CYS PHE ALA VAL ASP THR LYS VAL SEQRES 2 A 162 ILE ASP SER ARG LEU VAL GLY GLU GLY SER SER VAL ARG SEQRES 3 A 162 ARG ARG ARG GLN CYS LEU VAL CYS ASN GLU ARG PHE THR SEQRES 4 A 162 THR PHE GLU VAL ALA GLU LEU VAL MET PRO ARG VAL VAL SEQRES 5 A 162 LYS SER ASN ASP VAL ARG GLU PRO PHE ASN GLU GLU LYS SEQRES 6 A 162 LEU ARG SER GLY MET LEU ARG ALA LEU GLU LYS ARG PRO SEQRES 7 A 162 VAL SER SER ASP ASP VAL GLU MET ALA ILE ASN HIS ILE SEQRES 8 A 162 LYS SER GLN LEU ARG ALA THR GLY GLU ARG GLU VAL PRO SEQRES 9 A 162 SER LYS MET ILE GLY ASN LEU VAL MET GLU GLN LEU LYS SEQRES 10 A 162 LYS LEU ASP LYS VAL ALA TYR ILE ARG PHE ALA SER VAL SEQRES 11 A 162 TYR ARG SER PHE GLU ASP ILE LYS ASP PHE GLY GLU GLU SEQRES 12 A 162 ILE ALA ARG LEU GLU ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 13 A 162 HIS HIS HIS HIS HIS HIS SEQRES 1 B 162 MET HIS CYS PRO PHE CYS PHE ALA VAL ASP THR LYS VAL SEQRES 2 B 162 ILE ASP SER ARG LEU VAL GLY GLU GLY SER SER VAL ARG SEQRES 3 B 162 ARG ARG ARG GLN CYS LEU VAL CYS ASN GLU ARG PHE THR SEQRES 4 B 162 THR PHE GLU VAL ALA GLU LEU VAL MET PRO ARG VAL VAL SEQRES 5 B 162 LYS SER ASN ASP VAL ARG GLU PRO PHE ASN GLU GLU LYS SEQRES 6 B 162 LEU ARG SER GLY MET LEU ARG ALA LEU GLU LYS ARG PRO SEQRES 7 B 162 VAL SER SER ASP ASP VAL GLU MET ALA ILE ASN HIS ILE SEQRES 8 B 162 LYS SER GLN LEU ARG ALA THR GLY GLU ARG GLU VAL PRO SEQRES 9 B 162 SER LYS MET ILE GLY ASN LEU VAL MET GLU GLN LEU LYS SEQRES 10 B 162 LYS LEU ASP LYS VAL ALA TYR ILE ARG PHE ALA SER VAL SEQRES 11 B 162 TYR ARG SER PHE GLU ASP ILE LYS ASP PHE GLY GLU GLU SEQRES 12 B 162 ILE ALA ARG LEU GLU ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 13 B 162 HIS HIS HIS HIS HIS HIS HET DTP A 200 30 HET ADP A 201 27 HET ZN A 202 1 HET MG A 203 1 HET DTP B 200 30 HET ADP B 201 27 HET ZN B 202 1 HET MG B 203 1 HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 3 DTP 2(C10 H16 N5 O12 P3) FORMUL 4 ADP 2(C10 H15 N5 O10 P2) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 MG 2(MG 2+) FORMUL 11 HOH *161(H2 O) HELIX 1 AA1 ASN A 62 LEU A 74 1 13 HELIX 2 AA2 SER A 80 THR A 98 1 19 HELIX 3 AA3 SER A 105 ASP A 120 1 16 HELIX 4 AA4 ASP A 120 ARG A 132 1 13 HELIX 5 AA5 ILE A 137 ASP A 149 1 13 HELIX 6 AA6 GLY B 20 SER B 23 5 4 HELIX 7 AA7 ASN B 62 LEU B 74 1 13 HELIX 8 AA8 SER B 80 GLY B 99 1 20 HELIX 9 AA9 SER B 105 ASP B 120 1 16 HELIX 10 AB1 ASP B 120 ARG B 132 1 13 HELIX 11 AB2 ASP B 136 LEU B 147 1 12 SHEET 1 AA1 3 THR A 11 ARG A 17 0 SHEET 2 AA1 3 SER A 24 CYS A 31 -1 O ARG A 28 N ILE A 14 SHEET 3 AA1 3 ARG A 37 VAL A 43 -1 O THR A 40 N ARG A 27 SHEET 1 AA2 3 ARG A 58 GLU A 59 0 SHEET 2 AA2 3 ARG A 50 VAL A 52 -1 N VAL A 51 O GLU A 59 SHEET 3 AA2 3 GLU A 102 PRO A 104 1 O VAL A 103 N ARG A 50 SHEET 1 AA3 3 LYS B 12 VAL B 19 0 SHEET 2 AA3 3 SER B 24 GLN B 30 -1 O ARG B 26 N ARG B 17 SHEET 3 AA3 3 ARG B 37 GLU B 42 -1 O THR B 40 N ARG B 27 SHEET 1 AA4 3 ARG B 58 GLU B 59 0 SHEET 2 AA4 3 ARG B 50 VAL B 52 -1 N VAL B 51 O GLU B 59 SHEET 3 AA4 3 GLU B 102 PRO B 104 1 O VAL B 103 N ARG B 50 LINK SG CYS A 3 ZN ZN A 202 1555 1555 2.18 LINK SG CYS A 6 ZN ZN A 202 1555 1555 2.45 LINK SG CYS A 31 ZN ZN A 202 1555 1555 2.17 LINK SG CYS A 34 ZN ZN A 202 1555 1555 2.38 LINK O2G DTP A 200 MG MG A 203 1555 1555 2.07 LINK O2B DTP A 200 MG MG A 203 1555 1555 1.93 LINK O2A DTP A 200 MG MG A 203 1555 1555 1.93 LINK O3B ADP A 201 MG MG A 203 1555 1555 2.50 LINK O2A ADP A 201 MG MG A 203 1555 1555 2.56 LINK MG MG A 203 O HOH A 301 1555 1555 1.94 LINK SG CYS B 3 ZN ZN B 202 1555 1555 2.18 LINK SG CYS B 6 ZN ZN B 202 1555 1555 2.27 LINK SG CYS B 31 ZN ZN B 202 1555 1555 2.34 LINK SG CYS B 34 ZN ZN B 202 1555 1555 2.44 LINK O3G DTP B 200 MG MG B 203 1555 1555 1.94 LINK O2B DTP B 200 MG MG B 203 1555 1555 1.93 LINK O2A DTP B 200 MG MG B 203 1555 1555 1.94 LINK O1B ADP B 201 MG MG B 203 1555 1555 1.93 LINK O2A ADP B 201 MG MG B 203 1555 1555 2.58 LINK MG MG B 203 O HOH B 302 1555 1555 1.93 CRYST1 147.126 147.126 85.805 90.00 90.00 120.00 P 62 2 2 24 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 0.006797 0.003924 0.000000 0.00000 SCALE2 0.000000 0.007848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011654 0.00000 CONECT 24 2464 CONECT 48 2464 CONECT 245 2464 CONECT 266 2464 CONECT 1227 2523 CONECT 1251 2523 CONECT 1448 2523 CONECT 1469 2523 CONECT 2407 2408 2409 2410 2414 CONECT 2408 2407 CONECT 2409 2407 2465 CONECT 2410 2407 CONECT 2411 2412 2413 2414 2418 CONECT 2412 2411 CONECT 2413 2411 2465 CONECT 2414 2407 2411 CONECT 2415 2416 2417 2418 2419 CONECT 2416 2415 CONECT 2417 2415 2465 CONECT 2418 2411 2415 CONECT 2419 2415 2420 CONECT 2420 2419 2421 CONECT 2421 2420 2422 2423 CONECT 2422 2421 2426 CONECT 2423 2421 2424 2425 CONECT 2424 2423 CONECT 2425 2423 2426 CONECT 2426 2422 2425 2427 CONECT 2427 2426 2428 2436 CONECT 2428 2427 2429 CONECT 2429 2428 2430 CONECT 2430 2429 2431 2436 CONECT 2431 2430 2432 2433 CONECT 2432 2431 CONECT 2433 2431 2434 CONECT 2434 2433 2435 CONECT 2435 2434 2436 CONECT 2436 2427 2430 2435 CONECT 2437 2438 2439 2440 2444 CONECT 2438 2437 CONECT 2439 2437 CONECT 2440 2437 2465 CONECT 2441 2442 2443 2444 2445 CONECT 2442 2441 CONECT 2443 2441 2465 CONECT 2444 2437 2441 CONECT 2445 2441 2446 CONECT 2446 2445 2447 CONECT 2447 2446 2448 2449 CONECT 2448 2447 2453 CONECT 2449 2447 2450 2451 CONECT 2450 2449 CONECT 2451 2449 2452 2453 CONECT 2452 2451 CONECT 2453 2448 2451 2454 CONECT 2454 2453 2455 2463 CONECT 2455 2454 2456 CONECT 2456 2455 2457 CONECT 2457 2456 2458 2463 CONECT 2458 2457 2459 2460 CONECT 2459 2458 CONECT 2460 2458 2461 CONECT 2461 2460 2462 CONECT 2462 2461 2463 CONECT 2463 2454 2457 2462 CONECT 2464 24 48 245 266 CONECT 2465 2409 2413 2417 2440 CONECT 2465 2443 2525 CONECT 2466 2467 2468 2469 2473 CONECT 2467 2466 CONECT 2468 2466 CONECT 2469 2466 2524 CONECT 2470 2471 2472 2473 2477 CONECT 2471 2470 CONECT 2472 2470 2524 CONECT 2473 2466 2470 CONECT 2474 2475 2476 2477 2478 CONECT 2475 2474 CONECT 2476 2474 2524 CONECT 2477 2470 2474 CONECT 2478 2474 2479 CONECT 2479 2478 2480 CONECT 2480 2479 2481 2482 CONECT 2481 2480 2485 CONECT 2482 2480 2483 2484 CONECT 2483 2482 CONECT 2484 2482 2485 CONECT 2485 2481 2484 2486 CONECT 2486 2485 2487 2495 CONECT 2487 2486 2488 CONECT 2488 2487 2489 CONECT 2489 2488 2490 2495 CONECT 2490 2489 2491 2492 CONECT 2491 2490 CONECT 2492 2490 2493 CONECT 2493 2492 2494 CONECT 2494 2493 2495 CONECT 2495 2486 2489 2494 CONECT 2496 2497 2498 2499 2503 CONECT 2497 2496 2524 CONECT 2498 2496 CONECT 2499 2496 CONECT 2500 2501 2502 2503 2504 CONECT 2501 2500 CONECT 2502 2500 2524 CONECT 2503 2496 2500 CONECT 2504 2500 2505 CONECT 2505 2504 2506 CONECT 2506 2505 2507 2508 CONECT 2507 2506 2512 CONECT 2508 2506 2509 2510 CONECT 2509 2508 CONECT 2510 2508 2511 2512 CONECT 2511 2510 CONECT 2512 2507 2510 2513 CONECT 2513 2512 2514 2522 CONECT 2514 2513 2515 CONECT 2515 2514 2516 CONECT 2516 2515 2517 2522 CONECT 2517 2516 2518 2519 CONECT 2518 2517 CONECT 2519 2517 2520 CONECT 2520 2519 2521 CONECT 2521 2520 2522 CONECT 2522 2513 2516 2521 CONECT 2523 1227 1251 1448 1469 CONECT 2524 2469 2472 2476 2497 CONECT 2524 2502 2580 CONECT 2525 2465 CONECT 2580 2524 MASTER 423 0 8 11 12 0 0 6 2683 2 130 26 END