HEADER DNA BINDING PROTEIN 28-JAN-25 9N2G TITLE STRUCTURE OF APO MTB NAPA(16-90) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIS FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: U, A; COMPND 4 SYNONYM: NAPA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: A4S10_00456, DKC2_0461, DSI80_09725, ERS007657_03567, SOURCE 5 ERS007679_01808, ERS007681_02029, ERS007688_00846, ERS007718_00086, SOURCE 6 ERS007741_01318, ERS027646_00220, ERS027659_01205, ERS027661_02888, SOURCE 7 ERS053720_01018; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOID ASSOCIATED PROTEIN, NAP, NAPA, MYCOBACTERIUM TUBERCULOSIS, KEYWDS 2 DNA BRIDGING, DNA COATING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER REVDAT 1 22-OCT-25 9N2G 0 JRNL AUTH M.A.SCHUMACHER JRNL TITL STRUCTURE OF APO MTB NAPA(16-90) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 5001 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.160 REMARK 3 FREE R VALUE TEST SET COUNT : 508 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 38.4400 - 3.7900 0.95 1111 127 0.1950 0.2029 REMARK 3 2 3.7900 - 3.0100 0.97 1107 123 0.2453 0.2585 REMARK 3 3 3.0100 - 2.6300 0.99 1135 129 0.2725 0.3098 REMARK 3 4 2.6300 - 2.3900 0.99 1140 129 0.2694 0.2839 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 7 REMARK 3 ANGLE : 1.021 7 REMARK 3 CHIRALITY : 0.053 172 REMARK 3 PLANARITY : 0.035 204 REMARK 3 DIHEDRAL : 17.872 453 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -10.9222 -30.7201 0.2475 REMARK 3 T TENSOR REMARK 3 T11: 0.2398 T22: 0.4253 REMARK 3 T33: 0.2252 T12: -0.0027 REMARK 3 T13: 0.0053 T23: -0.0021 REMARK 3 L TENSOR REMARK 3 L11: 1.5792 L22: 3.3375 REMARK 3 L33: 0.0798 L12: -0.4580 REMARK 3 L13: 0.0354 L23: -0.4000 REMARK 3 S TENSOR REMARK 3 S11: -0.0215 S12: -0.1288 S13: -0.1242 REMARK 3 S21: 0.2036 S22: 0.0703 S23: 0.1532 REMARK 3 S31: -0.0148 S32: -0.1406 S33: -0.0716 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 9N2G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000292361. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-24 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 : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS V7.0.078 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5554 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.390 REMARK 200 RESOLUTION RANGE LOW (A) : 38.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21800 REMARK 200 FOR SHELL : 2.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23%PEG 3350, 0.1 M SODIUM THIOCYANATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 13.24517 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.17950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.51636 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 13.24517 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.17950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 30.51636 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: 3440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: U, 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 U 14 REMARK 465 SER U 15 REMARK 465 HIS U 16 REMARK 465 MET U 17 REMARK 465 ALA U 18 REMARK 465 ASP U 19 REMARK 465 ALA U 91 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 MET A 17 REMARK 465 ALA A 18 REMARK 465 ASP A 19 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 LYS U 47 CG CD CE NZ REMARK 470 ASN U 62 CG OD1 ND2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 LEU A 71 CG CD1 CD2 REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 ARG A 83 CG CD NE CZ NH1 NH2 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 NH2 ARG A 33 O HOH A 101 2.19 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 NH1 ARG U 88 NH1 ARG U 88 2455 2.07 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 GLN U 89 -69.10 -96.99 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 U 56 0.25 SIDE CHAIN REMARK 500 ARG A 33 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF1 9N2G U 18 91 UNP A0A045J292_MYCTX DBREF2 9N2G U A0A045J292 18 91 DBREF1 9N2G A 18 91 UNP A0A045J292_MYCTX DBREF2 9N2G A A0A045J292 18 91 SEQADV 9N2G GLY U 14 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G SER U 15 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G HIS U 16 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G MET U 17 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G GLY A 14 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G SER A 15 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G HIS A 16 UNP A0A045J29 EXPRESSION TAG SEQADV 9N2G MET A 17 UNP A0A045J29 EXPRESSION TAG SEQRES 1 U 78 GLY SER HIS MET ALA ASP GLY LEU THR ARG ARG GLU HIS SEQRES 2 U 78 ASP ILE LEU ALA PHE GLU ARG GLN TRP TRP LYS PHE ALA SEQRES 3 U 78 GLY VAL LYS GLU GLU ALA ILE LYS GLU LEU PHE SER MET SEQRES 4 U 78 SER ALA THR ARG TYR TYR GLN VAL LEU ASN ALA LEU VAL SEQRES 5 U 78 ASP ARG PRO GLU ALA LEU ALA ALA ASP PRO MET LEU VAL SEQRES 6 U 78 LYS ARG LEU ARG ARG LEU ARG ALA SER ARG GLN LYS ALA SEQRES 1 A 78 GLY SER HIS MET ALA ASP GLY LEU THR ARG ARG GLU HIS SEQRES 2 A 78 ASP ILE LEU ALA PHE GLU ARG GLN TRP TRP LYS PHE ALA SEQRES 3 A 78 GLY VAL LYS GLU GLU ALA ILE LYS GLU LEU PHE SER MET SEQRES 4 A 78 SER ALA THR ARG TYR TYR GLN VAL LEU ASN ALA LEU VAL SEQRES 5 A 78 ASP ARG PRO GLU ALA LEU ALA ALA ASP PRO MET LEU VAL SEQRES 6 A 78 LYS ARG LEU ARG ARG LEU ARG ALA SER ARG GLN LYS ALA FORMUL 3 HOH *15(H2 O) HELIX 1 AA1 THR U 22 PHE U 50 1 29 HELIX 2 AA2 SER U 53 ASP U 66 1 14 HELIX 3 AA3 ARG U 67 ASP U 74 1 8 HELIX 4 AA4 ASP U 74 LYS U 90 1 17 HELIX 5 AA5 THR A 22 PHE A 50 1 29 HELIX 6 AA6 SER A 53 ASP A 66 1 14 HELIX 7 AA7 ARG A 67 ASP A 74 1 8 HELIX 8 AA8 ASP A 74 ALA A 91 1 18 CRYST1 41.900 50.359 62.948 90.00 104.17 90.00 I 1 2 1 8 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 0.023866 0.000000 0.006026 0.00000 SCALE2 0.000000 0.019857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016385 0.00000 MASTER 306 0 0 8 0 0 0 6 1184 2 0 12 END