HEADER HYDROLASE 19-OCT-25 9X8A TITLE THE STRUCTURE OF THE M.TB MAZF-MT9 VARIANT (A2-P114) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ENDORIBONUCLEASE MAZF7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TOXIN MAZF7; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: MAZF7, RV2063A; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXIN-ANTITOXIN FAMILY, MAZF, MYCOBACTERIUM TUBERCULOSIS, TRNA, KEYWDS 2 CONFORMATIONAL DYNAMICS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,Y.YU,T.WANG REVDAT 1 28-OCT-26 9X8A 0 JRNL AUTH W.XIE JRNL TITL THE C-TERMINAL EXTENSION OF M.TB MAZF-MT9 CONFERS FUNCTIONAL JRNL TITL 2 AND CONFORMATIONAL DIVERSITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 13297 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 649 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 43.8200 - 3.3000 0.94 2704 118 0.1585 0.1881 REMARK 3 2 3.3000 - 2.6200 0.95 2649 155 0.1832 0.2571 REMARK 3 3 2.6200 - 2.2900 1.00 2794 151 0.1890 0.3199 REMARK 3 4 2.2900 - 2.0800 0.85 2364 129 0.1967 0.2160 REMARK 3 5 2.0800 - 1.9300 0.76 2137 96 0.3320 0.4240 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) : 0.287 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.061 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.66 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 1663 REMARK 3 ANGLE : 0.945 2273 REMARK 3 CHIRALITY : 0.053 284 REMARK 3 PLANARITY : 0.009 298 REMARK 3 DIHEDRAL : 13.643 625 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 9X8A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 43.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 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 (%): 39.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG6000, 0.1 M TRIS-HCL 8.5, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 31.52750 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: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 PRO A -1 REMARK 465 GLU A 0 REMARK 465 LEU A 1 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 GLU B 0 REMARK 465 LEU B 1 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 A 24 CG CD CE NZ REMARK 470 SER A 52 OG REMARK 470 SER A 53 OG REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 72 CG OD1 OD2 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 B 54 O HOH B 201 2.06 REMARK 500 O HOH A 208 O HOH A 236 2.11 REMARK 500 O HOH A 247 O HOH A 258 2.11 REMARK 500 OD1 ASP A 41 O HOH A 201 2.11 REMARK 500 O HOH B 284 O HOH B 289 2.18 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 233 O HOH B 207 2646 2.17 REMARK 500 O HOH B 204 O HOH B 258 2555 2.17 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 LYS A 24 -163.63 63.36 REMARK 500 LYS B 24 -164.65 65.17 REMARK 500 SER B 55 55.11 -90.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 9X8A A 2 114 UNP P0CL62 MAZF7_MYCTU 2 114 DBREF 9X8A B 2 114 UNP P0CL62 MAZF7_MYCTU 2 114 SEQADV 9X8A GLY A -2 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A PRO A -1 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A GLU A 0 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A LEU A 1 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A GLY B -2 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A PRO B -1 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A GLU B 0 UNP P0CL62 EXPRESSION TAG SEQADV 9X8A LEU B 1 UNP P0CL62 EXPRESSION TAG SEQRES 1 A 117 GLY PRO GLU LEU ALA GLU PRO ARG ARG GLY ASP LEU TRP SEQRES 2 A 117 LEU VAL SER LEU GLY ALA ALA ARG ALA GLY GLU PRO GLY SEQRES 3 A 117 LYS HIS ARG PRO ALA VAL VAL VAL SER VAL ASP GLU LEU SEQRES 4 A 117 LEU THR GLY ILE ASP ASP GLU LEU VAL VAL VAL VAL PRO SEQRES 5 A 117 VAL SER SER SER ARG SER ARG THR PRO LEU ARG PRO PRO SEQRES 6 A 117 VAL ALA PRO SER GLU GLY VAL ALA ALA ASP SER VAL ALA SEQRES 7 A 117 VAL CYS ARG GLY VAL ARG ALA VAL ALA ARG ALA ARG LEU SEQRES 8 A 117 VAL GLU ARG LEU GLY ALA LEU LYS PRO ALA THR MET ARG SEQRES 9 A 117 ALA ILE GLU ASN ALA LEU THR LEU ILE LEU GLY LEU PRO SEQRES 1 B 117 GLY PRO GLU LEU ALA GLU PRO ARG ARG GLY ASP LEU TRP SEQRES 2 B 117 LEU VAL SER LEU GLY ALA ALA ARG ALA GLY GLU PRO GLY SEQRES 3 B 117 LYS HIS ARG PRO ALA VAL VAL VAL SER VAL ASP GLU LEU SEQRES 4 B 117 LEU THR GLY ILE ASP ASP GLU LEU VAL VAL VAL VAL PRO SEQRES 5 B 117 VAL SER SER SER ARG SER ARG THR PRO LEU ARG PRO PRO SEQRES 6 B 117 VAL ALA PRO SER GLU GLY VAL ALA ALA ASP SER VAL ALA SEQRES 7 B 117 VAL CYS ARG GLY VAL ARG ALA VAL ALA ARG ALA ARG LEU SEQRES 8 B 117 VAL GLU ARG LEU GLY ALA LEU LYS PRO ALA THR MET ARG SEQRES 9 B 117 ALA ILE GLU ASN ALA LEU THR LEU ILE LEU GLY LEU PRO FORMUL 3 HOH *153(H2 O) HELIX 1 AA1 VAL A 33 LEU A 37 5 5 HELIX 2 AA2 ALA A 64 GLY A 68 5 5 HELIX 3 AA3 CYS A 77 VAL A 80 5 4 HELIX 4 AA4 LYS A 96 LEU A 111 1 16 HELIX 5 AA5 VAL B 33 LEU B 37 5 5 HELIX 6 AA6 ALA B 64 GLY B 68 5 5 HELIX 7 AA7 CYS B 77 VAL B 80 5 4 HELIX 8 AA8 LYS B 96 LEU B 111 1 16 SHEET 1 AA1 4 PRO A 62 VAL A 63 0 SHEET 2 AA1 4 SER A 73 ALA A 75 -1 O SER A 73 N VAL A 63 SHEET 3 AA1 4 LEU A 44 SER A 51 -1 N SER A 51 O VAL A 74 SHEET 4 AA1 4 ARG A 81 ALA A 84 -1 O VAL A 83 N VAL A 45 SHEET 1 AA2 6 PRO A 62 VAL A 63 0 SHEET 2 AA2 6 SER A 73 ALA A 75 -1 O SER A 73 N VAL A 63 SHEET 3 AA2 6 LEU A 44 SER A 51 -1 N SER A 51 O VAL A 74 SHEET 4 AA2 6 HIS A 25 VAL A 30 -1 N PRO A 27 O VAL A 50 SHEET 5 AA2 6 ASP A 8 SER A 13 -1 N VAL A 12 O ARG A 26 SHEET 6 AA2 6 LEU A 88 ALA A 94 -1 O GLU A 90 N LEU A 11 SHEET 1 AA3 4 PRO B 62 VAL B 63 0 SHEET 2 AA3 4 SER B 73 ALA B 75 -1 O SER B 73 N VAL B 63 SHEET 3 AA3 4 LEU B 44 SER B 51 -1 N SER B 51 O VAL B 74 SHEET 4 AA3 4 ARG B 81 ALA B 84 -1 O VAL B 83 N VAL B 45 SHEET 1 AA4 6 PRO B 62 VAL B 63 0 SHEET 2 AA4 6 SER B 73 ALA B 75 -1 O SER B 73 N VAL B 63 SHEET 3 AA4 6 LEU B 44 SER B 51 -1 N SER B 51 O VAL B 74 SHEET 4 AA4 6 HIS B 25 VAL B 30 -1 N PRO B 27 O VAL B 50 SHEET 5 AA4 6 ASP B 8 SER B 13 -1 N TRP B 10 O ALA B 28 SHEET 6 AA4 6 LEU B 88 ALA B 94 -1 O GLU B 90 N LEU B 11 CRYST1 35.847 63.055 45.504 90.00 105.63 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 0.027896 0.000000 0.007802 0.00000 SCALE2 0.000000 0.015859 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022819 0.00000 MASTER 268 0 0 8 20 0 0 6 1792 2 0 18 END