HEADER GTPASE ACTIVATING PROTEIN 14-NOV-24 9HEF TITLE CRYSTAL STRUCTURE OF MFPD FROM MYCOBACTERIUM TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE INHIBITOR RV3364C; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: RV3364C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GAP PROTEIN, UNKNOWN FUNCTION, GTPASE ACTIVATING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MICALETTO,A.HAOUZ,S.PETRELLA REVDAT 1 27-MAY-26 9HEF 0 JRNL AUTH T.MICALETTO,S.PETRELLA JRNL TITL CRYSTAL STRUCTURE OF MFPD FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 35875 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.40 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9HEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1292142619. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98011 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35875 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NA ACETATE, 60 % MPD, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.82500 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 -2 REMARK 465 ALA A -1 REMARK 465 MET A 0 REMARK 465 GLY A 1 REMARK 465 LYS A 2 REMARK 465 ALA A 3 REMARK 465 ARG A 4 REMARK 465 LEU A 5 REMARK 465 PRO A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 VAL A 125 REMARK 465 GLN A 126 REMARK 465 SER A 127 REMARK 465 CYS A 128 REMARK 465 ARG A 129 REMARK 465 ARG A 130 REMARK 465 GLY B -2 REMARK 465 ALA B -1 REMARK 465 MET B 0 REMARK 465 GLY B 1 REMARK 465 LYS B 2 REMARK 465 SER B 127 REMARK 465 CYS B 128 REMARK 465 ARG B 129 REMARK 465 ARG B 130 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 VAL A 124 CG1 CG2 REMARK 470 ARG B 4 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 124 CG1 CG2 REMARK 470 VAL B 125 CG1 CG2 REMARK 470 GLN B 126 CG CD OE1 NE2 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 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 18 O REMARK 620 2 VAL A 24 O 87.4 REMARK 620 3 HOH A 301 O 92.6 169.3 REMARK 620 4 HOH A 302 O 87.4 81.6 87.7 REMARK 620 5 HOH A 319 O 88.7 90.8 99.9 171.6 REMARK 620 6 HOH A 321 O 157.1 72.5 105.1 79.1 102.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 18 O REMARK 620 2 VAL B 21 O 101.9 REMARK 620 3 VAL B 24 O 74.3 104.9 REMARK 620 4 HOH B 307 O 63.8 165.6 73.4 REMARK 620 N 1 2 3 DBREF 9HEF A 2 130 UNP O50393 SPI_MYCTU 2 130 DBREF 9HEF B 2 130 UNP O50393 SPI_MYCTU 2 130 SEQADV 9HEF GLY A -2 UNP O50393 EXPRESSION TAG SEQADV 9HEF ALA A -1 UNP O50393 EXPRESSION TAG SEQADV 9HEF MET A 0 UNP O50393 EXPRESSION TAG SEQADV 9HEF GLY A 1 UNP O50393 EXPRESSION TAG SEQADV 9HEF GLY B -2 UNP O50393 EXPRESSION TAG SEQADV 9HEF ALA B -1 UNP O50393 EXPRESSION TAG SEQADV 9HEF MET B 0 UNP O50393 EXPRESSION TAG SEQADV 9HEF GLY B 1 UNP O50393 EXPRESSION TAG SEQRES 1 A 133 GLY ALA MET GLY LYS ALA ARG LEU PRO ASP SER PRO LEU SEQRES 2 A 133 ASP TRP LEU VAL SER LYS PHE ALA ARG GLU VAL PRO GLY SEQRES 3 A 133 VAL ALA HIS ALA LEU LEU VAL SER VAL ASP GLY LEU PRO SEQRES 4 A 133 VAL ALA ALA SER GLU HIS LEU PRO ARG GLU ARG ALA ASP SEQRES 5 A 133 GLN LEU ALA ALA VAL THR SER GLY LEU ALA SER LEU ALA SEQRES 6 A 133 GLY GLY ALA ALA GLN LEU PHE ASP GLY GLY GLN VAL LEU SEQRES 7 A 133 GLN SER VAL VAL GLU MET GLN ASN GLY TYR LEU LEU LEU SEQRES 8 A 133 MET GLN VAL GLY ASP GLY SER ALA LEU ALA ALA LEU ALA SEQRES 9 A 133 ALA THR GLY CYS ASP ILE GLY GLN ILE GLY TYR GLU MET SEQRES 10 A 133 ALA ILE LEU VAL GLU ARG VAL GLY GLY VAL VAL GLN SER SEQRES 11 A 133 CYS ARG ARG SEQRES 1 B 133 GLY ALA MET GLY LYS ALA ARG LEU PRO ASP SER PRO LEU SEQRES 2 B 133 ASP TRP LEU VAL SER LYS PHE ALA ARG GLU VAL PRO GLY SEQRES 3 B 133 VAL ALA HIS ALA LEU LEU VAL SER VAL ASP GLY LEU PRO SEQRES 4 B 133 VAL ALA ALA SER GLU HIS LEU PRO ARG GLU ARG ALA ASP SEQRES 5 B 133 GLN LEU ALA ALA VAL THR SER GLY LEU ALA SER LEU ALA SEQRES 6 B 133 GLY GLY ALA ALA GLN LEU PHE ASP GLY GLY GLN VAL LEU SEQRES 7 B 133 GLN SER VAL VAL GLU MET GLN ASN GLY TYR LEU LEU LEU SEQRES 8 B 133 MET GLN VAL GLY ASP GLY SER ALA LEU ALA ALA LEU ALA SEQRES 9 B 133 ALA THR GLY CYS ASP ILE GLY GLN ILE GLY TYR GLU MET SEQRES 10 B 133 ALA ILE LEU VAL GLU ARG VAL GLY GLY VAL VAL GLN SER SEQRES 11 B 133 CYS ARG ARG HET NA A 201 1 HET EDO A 202 4 HET EDO A 203 4 HET NA B 201 1 HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NA 2(NA 1+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 HOH *48(H2 O) HELIX 1 AA1 PRO A 9 VAL A 21 1 13 HELIX 2 AA2 PRO A 44 PHE A 69 1 26 HELIX 3 AA3 ASP A 106 VAL A 124 1 19 HELIX 4 AA4 SER B 8 VAL B 21 1 14 HELIX 5 AA5 PRO B 44 PHE B 69 1 26 HELIX 6 AA6 ASP B 106 VAL B 125 1 20 SHEET 1 AA110 PRO A 36 ALA A 39 0 SHEET 2 AA110 VAL A 24 VAL A 30 -1 N LEU A 29 O VAL A 37 SHEET 3 AA110 ALA A 96 ALA A 101 -1 O ALA A 96 N VAL A 30 SHEET 4 AA110 GLY A 84 GLN A 90 -1 N MET A 89 O LEU A 97 SHEET 5 AA110 VAL A 74 MET A 81 -1 N MET A 81 O GLY A 84 SHEET 6 AA110 VAL B 74 MET B 81 -1 O GLU B 80 N GLN A 76 SHEET 7 AA110 GLY B 84 GLN B 90 -1 O GLY B 84 N MET B 81 SHEET 8 AA110 ALA B 96 ALA B 101 -1 O LEU B 97 N MET B 89 SHEET 9 AA110 VAL B 24 VAL B 30 -1 N VAL B 30 O ALA B 96 SHEET 10 AA110 PRO B 36 ALA B 39 -1 O ALA B 38 N LEU B 29 LINK O ALA A 18 NA NA A 201 1555 1555 2.36 LINK O VAL A 24 NA NA A 201 1555 1555 2.47 LINK NA NA A 201 O HOH A 301 1555 1555 3.06 LINK NA NA A 201 O HOH A 302 1555 1555 2.46 LINK NA NA A 201 O HOH A 319 1555 1555 2.30 LINK NA NA A 201 O HOH A 321 1555 1555 2.73 LINK O ALA B 18 NA NA B 201 1555 1555 2.60 LINK O VAL B 21 NA NA B 201 1555 1555 2.41 LINK O VAL B 24 NA NA B 201 1555 1555 2.75 LINK NA NA B 201 O HOH B 307 1555 1555 2.46 CRYST1 40.735 73.650 49.269 90.00 111.39 90.00 P 1 21 1 4 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 0.024549 0.000000 0.009613 0.00000 SCALE2 0.000000 0.013578 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021797 0.00000 CONECT 82 1704 CONECT 125 1704 CONECT 948 1713 CONECT 973 1713 CONECT 991 1713 CONECT 1704 82 125 1714 1715 CONECT 1704 1732 1734 CONECT 1705 1706 1707 CONECT 1706 1705 CONECT 1707 1705 1708 CONECT 1708 1707 CONECT 1709 1710 1711 CONECT 1710 1709 CONECT 1711 1709 1712 CONECT 1712 1711 CONECT 1713 948 973 991 1744 CONECT 1714 1704 CONECT 1715 1704 CONECT 1732 1704 CONECT 1734 1704 CONECT 1744 1713 MASTER 251 0 4 6 10 0 0 6 1759 2 21 22 END