HEADER HYDROLASE 20-OCT-25 9X9H TITLE THE STRUCTURE OF THE M.TB MAZF-MT9 VARIANT (A2-G120) 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 9X9H 0 JRNL AUTH W.XIE,Y.YU,T.WANG 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. 2.15 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 3 NUMBER OF REFLECTIONS : 8617 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.380 REMARK 3 FREE R VALUE TEST SET COUNT : 464 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 21.0000 - 3.0900 0.91 2971 163 0.1806 0.2650 REMARK 3 2 3.0900 - 2.4600 0.99 3158 186 0.2306 0.2925 REMARK 3 3 2.4600 - 2.1500 0.63 2024 115 0.2050 0.2690 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) : 0.275 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.57 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 : 0.009 1599 REMARK 3 ANGLE : 1.035 2188 REMARK 3 CHIRALITY : 0.057 280 REMARK 3 PLANARITY : 0.012 283 REMARK 3 DIHEDRAL : 15.314 594 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 9X9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 24-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1300064844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-25 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 : 8649 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 36.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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 (%): 33.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 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 30.95800 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: 2510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 A 116 REMARK 465 PRO A 117 REMARK 465 GLU A 118 REMARK 465 ARG A 119 REMARK 465 GLY A 120 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 GLU B 0 REMARK 465 LEU B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 15 REMARK 465 ALA B 16 REMARK 465 ALA B 17 REMARK 465 ARG B 18 REMARK 465 ALA B 19 REMARK 465 GLY B 20 REMARK 465 GLU B 21 REMARK 465 PRO B 22 REMARK 465 GLY B 23 REMARK 465 GLY B 116 REMARK 465 PRO B 117 REMARK 465 GLU B 118 REMARK 465 ARG B 119 REMARK 465 GLY B 120 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 LEU A 14 CG CD1 CD2 REMARK 470 ARG A 18 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 SER A 66 OG REMARK 470 ARG B 5 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 41 CG OD1 OD2 REMARK 470 SER B 66 OG 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 O PRO A 58 O HOH A 201 2.16 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 -161.92 72.11 REMARK 500 PRO A 114 48.62 -101.94 REMARK 500 REMARK 500 REMARK: NULL DBREF 9X9H A 2 120 UNP P0CL62 MAZF7_MYCTU 2 120 DBREF 9X9H B 2 120 UNP P0CL62 MAZF7_MYCTU 2 120 SEQADV 9X9H GLY A -2 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H PRO A -1 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H GLU A 0 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H LEU A 1 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H GLY B -2 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H PRO B -1 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H GLU B 0 UNP P0CL62 EXPRESSION TAG SEQADV 9X9H LEU B 1 UNP P0CL62 EXPRESSION TAG SEQRES 1 A 123 GLY PRO GLU LEU ALA GLU PRO ARG ARG GLY ASP LEU TRP SEQRES 2 A 123 LEU VAL SER LEU GLY ALA ALA ARG ALA GLY GLU PRO GLY SEQRES 3 A 123 LYS HIS ARG PRO ALA VAL VAL VAL SER VAL ASP GLU LEU SEQRES 4 A 123 LEU THR GLY ILE ASP ASP GLU LEU VAL VAL VAL VAL PRO SEQRES 5 A 123 VAL SER SER SER ARG SER ARG THR PRO LEU ARG PRO PRO SEQRES 6 A 123 VAL ALA PRO SER GLU GLY VAL ALA ALA ASP SER VAL ALA SEQRES 7 A 123 VAL CYS ARG GLY VAL ARG ALA VAL ALA ARG ALA ARG LEU SEQRES 8 A 123 VAL GLU ARG LEU GLY ALA LEU LYS PRO ALA THR MET ARG SEQRES 9 A 123 ALA ILE GLU ASN ALA LEU THR LEU ILE LEU GLY LEU PRO SEQRES 10 A 123 THR GLY PRO GLU ARG GLY SEQRES 1 B 123 GLY PRO GLU LEU ALA GLU PRO ARG ARG GLY ASP LEU TRP SEQRES 2 B 123 LEU VAL SER LEU GLY ALA ALA ARG ALA GLY GLU PRO GLY SEQRES 3 B 123 LYS HIS ARG PRO ALA VAL VAL VAL SER VAL ASP GLU LEU SEQRES 4 B 123 LEU THR GLY ILE ASP ASP GLU LEU VAL VAL VAL VAL PRO SEQRES 5 B 123 VAL SER SER SER ARG SER ARG THR PRO LEU ARG PRO PRO SEQRES 6 B 123 VAL ALA PRO SER GLU GLY VAL ALA ALA ASP SER VAL ALA SEQRES 7 B 123 VAL CYS ARG GLY VAL ARG ALA VAL ALA ARG ALA ARG LEU SEQRES 8 B 123 VAL GLU ARG LEU GLY ALA LEU LYS PRO ALA THR MET ARG SEQRES 9 B 123 ALA ILE GLU ASN ALA LEU THR LEU ILE LEU GLY LEU PRO SEQRES 10 B 123 THR GLY PRO GLU ARG GLY FORMUL 3 HOH *46(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 GLY A 112 1 17 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 52 -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 52 -1 N SER A 51 O VAL A 74 SHEET 4 AA2 6 HIS A 25 VAL A 30 -1 N VAL A 29 O VAL A 48 SHEET 5 AA2 6 ASP A 8 SER A 13 -1 N TRP A 10 O ALA A 28 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 ARG B 26 VAL B 30 -1 N VAL B 29 O VAL B 48 SHEET 5 AA4 6 ASP B 8 VAL B 12 -1 N VAL B 12 O ARG B 26 SHEET 6 AA4 6 LEU B 88 ALA B 94 -1 O LEU B 92 N LEU B 9 CRYST1 36.238 61.916 42.032 90.00 92.41 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 0.027595 0.000000 0.001162 0.00000 SCALE2 0.000000 0.016151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023812 0.00000 MASTER 264 0 0 8 20 0 0 6 1623 2 0 20 END