HEADER CHAPERONE 05-JUL-23 8JZC TITLE CRYSTAL STRUCTURE OF GEOBACILLUS STEAROTHERMOPHILUS NARJ COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRATE REDUCTASE MOLYBDENUM COFACTOR ASSEMBLY CHAPERONE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS ATCC 7953; SOURCE 3 ORGANISM_TAXID: 937593; SOURCE 4 STRAIN: ATCC 7953; SOURCE 5 GENE: NARJ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS REDOX ENZYME MATURATION PROTEIN, CHAPERONE, NARJ SUBFAMILY EXPDTA X-RAY DIFFRACTION AUTHOR W.S.SONG,J.H.KIM,B.NAMGUNG,H.Y.CHO,H.B.OH,S.I.YOON REVDAT 1 15-MAY-24 8JZC 0 JRNL AUTH W.S.SONG,J.H.KIM,B.NAMGUNG,H.Y.CHO,H.SHIN,H.B.OH,N.C.HA, JRNL AUTH 2 S.I.YOON JRNL TITL COMPLEMENTARY HYDROPHOBIC INTERACTION OF THE REDOX ENZYME JRNL TITL 2 MATURATION PROTEIN NARJ WITH THE SIGNAL PEPTIDE OF THE JRNL TITL 3 RESPIRATORY NITRATE REDUCTASE NARG. JRNL REF INT.J.BIOL.MACROMOL. V. 262 29620 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 38262549 JRNL DOI 10.1016/J.IJBIOMAC.2024.129620 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 538 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3500 - 4.0500 0.99 2587 149 0.1788 0.2206 REMARK 3 2 4.0500 - 3.2100 0.99 2486 131 0.2164 0.2598 REMARK 3 3 3.2100 - 2.8100 0.99 2456 109 0.2882 0.3662 REMARK 3 4 2.8100 - 2.5500 0.99 2441 149 0.2919 0.3306 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.274 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 58.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1369 REMARK 3 ANGLE : 0.611 1867 REMARK 3 CHIRALITY : 0.040 210 REMARK 3 PLANARITY : 0.005 244 REMARK 3 DIHEDRAL : 14.879 815 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 69 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.6498 49.2177 98.4203 REMARK 3 T TENSOR REMARK 3 T11: 0.4231 T22: 0.3891 REMARK 3 T33: 0.3153 T12: 0.0488 REMARK 3 T13: 0.0567 T23: 0.0502 REMARK 3 L TENSOR REMARK 3 L11: 8.8094 L22: 5.0098 REMARK 3 L33: 7.4340 L12: 2.1322 REMARK 3 L13: 0.0536 L23: -0.9176 REMARK 3 S TENSOR REMARK 3 S11: 0.1143 S12: 0.1628 S13: 0.3817 REMARK 3 S21: 0.0346 S22: 0.0234 S23: 0.1231 REMARK 3 S31: -0.4030 S32: 0.0637 S33: -0.0961 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 70 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9480 50.0890 81.4958 REMARK 3 T TENSOR REMARK 3 T11: 0.7928 T22: 0.5375 REMARK 3 T33: 0.4325 T12: -0.0337 REMARK 3 T13: 0.0255 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 8.6254 L22: 1.7774 REMARK 3 L33: 3.7336 L12: 2.1097 REMARK 3 L13: -4.9776 L23: -0.1824 REMARK 3 S TENSOR REMARK 3 S11: 0.2476 S12: -0.2740 S13: -0.2765 REMARK 3 S21: 0.0903 S22: -0.0265 S23: -0.0280 REMARK 3 S31: 0.4312 S32: -0.4368 S33: -0.2062 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 176 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5129 59.1500 91.2541 REMARK 3 T TENSOR REMARK 3 T11: 0.8985 T22: 0.5092 REMARK 3 T33: 0.4470 T12: -0.0206 REMARK 3 T13: 0.1330 T23: 0.0306 REMARK 3 L TENSOR REMARK 3 L11: 8.9251 L22: 3.0377 REMARK 3 L33: 5.2102 L12: 2.1975 REMARK 3 L13: -1.7137 L23: -0.6968 REMARK 3 S TENSOR REMARK 3 S11: 0.0050 S12: -0.0511 S13: 0.8199 REMARK 3 S21: 0.1125 S22: 0.1806 S23: 0.1178 REMARK 3 S31: -1.2752 S32: 0.1799 S33: -0.1322 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8JZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-18 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) : 0.9794 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 : 10633 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50300 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: AUTOSOL REMARK 200 STARTING MODEL: IN-HOUSE MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, GLYCEROL, PEG 550, REMARK 280 TRIS, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -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 29.35167 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 58.70333 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 58.70333 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 29.35167 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: MONOMERIC 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 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 GLY A -5 REMARK 465 SER A -4 REMARK 465 ALA A -3 REMARK 465 LYS A -2 REMARK 465 ASP A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 THR A 84 REMARK 465 ASN A 85 REMARK 465 GLY A 86 REMARK 465 LEU A 177 REMARK 465 PRO A 178 REMARK 465 LYS A 179 REMARK 465 GLY A 180 REMARK 465 GLY A 181 REMARK 465 ALA A 182 REMARK 465 THR A 183 REMARK 465 ALA A 184 REMARK 465 TRP A 185 REMARK 465 PRO A 186 REMARK 465 ALA A 187 REMARK 465 ASN A 188 REMARK 465 PHE A 189 REMARK 465 SER A 190 REMARK 465 GLY A 191 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 ASN A 2 CG OD1 ND2 REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 ASP A 71 CG OD1 OD2 REMARK 470 LYS A 75 CG CD CE NZ REMARK 470 MET A 83 CG SD CE REMARK 470 VAL A 109 CG1 CG2 REMARK 470 ASP A 111 CG OD1 OD2 REMARK 470 GLN A 130 CG CD OE1 NE2 REMARK 470 GLU A 131 CG CD OE1 OE2 REMARK 470 THR A 175 OG1 CG2 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 PRO A 20 56.66 -92.04 REMARK 500 ASP A 21 -167.43 -75.24 REMARK 500 ASP A 111 45.07 -85.75 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8JZC A 1 191 UNP A0A0K9HWM0_GEOSE DBREF2 8JZC A A0A0K9HWM0 1 191 SEQADV 8JZC GLY A -5 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC SER A -4 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC ALA A -3 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC LYS A -2 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC ASP A -1 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC PRO A 0 UNP A0A0K9HWM EXPRESSION TAG SEQADV 8JZC ILE A 56 UNP A0A0K9HWM VAL 56 ENGINEERED MUTATION SEQRES 1 A 197 GLY SER ALA LYS ASP PRO MET ASN SER GLU GLN GLN GLN SEQRES 2 A 197 THR VAL PHE LEU CYS VAL SER TYR LEU LEU SER TYR PRO SEQRES 3 A 197 ASP GLU GLN TRP ALA GLU SER LEU PRO ASP CYS LEU ASP SEQRES 4 A 197 ALA ILE ARG SER LEU ASP ASP GLU THR VAL ARG ALA PRO SEQRES 5 A 197 LEU LEU ALA VAL ALA GLU GLN LEU ALA ILE THR PRO ALA SEQRES 6 A 197 ARG GLU ARG MET GLU GLN TYR VAL GLU THR PHE ASP PHE SEQRES 7 A 197 GLY LYS LYS THR ASN LEU TYR LEU THR TYR MET THR ASN SEQRES 8 A 197 GLY GLU GLN ARG GLU ARG GLY ILE GLU LEU VAL ALA LEU SEQRES 9 A 197 LYS ALA ARG TYR GLU ALA ALA GLY PHE ALA VAL SER ASP SEQRES 10 A 197 HIS GLU LEU PRO ASP TYR LEU PRO LEU MET LEU GLU TRP SEQRES 11 A 197 MET ALA TYR ALA ASP GLN GLU HIS THR THR ALA LEU LEU SEQRES 12 A 197 ALA ASP TYR ALA GLY HIS ILE ARG GLU ILE GLY ASP ARG SEQRES 13 A 197 LEU ALA ALA ALA GLY SER PRO TYR ALA GLN LEU PHE ASP SEQRES 14 A 197 ALA LEU ASN HIS THR PHE THR GLN LEU GLY VAL THR PRO SEQRES 15 A 197 LEU PRO LYS GLY GLY ALA THR ALA TRP PRO ALA ASN PHE SEQRES 16 A 197 SER GLY HELIX 1 AA1 ASN A 2 LEU A 17 1 16 HELIX 2 AA2 ASP A 21 GLU A 26 1 6 HELIX 3 AA3 SER A 27 SER A 37 1 11 HELIX 4 AA4 ASP A 40 ILE A 56 1 17 HELIX 5 AA5 PRO A 58 PHE A 70 1 13 HELIX 6 AA6 TYR A 79 MET A 83 5 5 HELIX 7 AA7 GLN A 88 ALA A 105 1 18 HELIX 8 AA8 TYR A 117 ALA A 128 1 12 HELIX 9 AA9 ASP A 129 ALA A 154 1 26 HELIX 10 AB1 TYR A 158 LEU A 172 1 15 CRYST1 78.514 78.514 88.055 90.00 90.00 120.00 P 31 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 0.012737 0.007353 0.000000 0.00000 SCALE2 0.000000 0.014707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011357 0.00000