HEADER BIOSYNTHETIC PROTEIN 18-MAY-25 9V0M TITLE ISOCHORISMATE SYNTHASE MENF COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCHORISMATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ISOCHORISMATE MUTASE; COMPND 5 EC: 5.4.4.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 GENE: MSMEG_1925; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOCHORISMATE SYNTHASE, MSMENF, MYCOLICIBACTERIUM SMEGMATIS., KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.SUN,Q.ZHANG,M.BARTLAM REVDAT 1 27-MAY-26 9V0M 0 JRNL AUTH L.SUN,Q.ZHANG,M.BARTLAM JRNL TITL ISOCHORISMATE SYNTHASE MENF JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 12752 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.247 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 612 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 45.7900 - 3.8900 0.91 3160 170 0.2125 0.2609 REMARK 3 2 3.8900 - 3.0900 0.93 3090 147 0.2450 0.3203 REMARK 3 3 3.0900 - 2.7000 0.93 3092 149 0.2971 0.3487 REMARK 3 4 2.7000 - 2.4500 0.86 2798 146 0.3333 0.3987 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) : 0.429 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.12 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 : 0.010 2682 REMARK 3 ANGLE : 1.251 3674 REMARK 3 CHIRALITY : 0.061 439 REMARK 3 PLANARITY : 0.010 489 REMARK 3 DIHEDRAL : 17.399 958 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): 17.8294 -3.9561 -12.2119 REMARK 3 T TENSOR REMARK 3 T11: 0.3194 T22: 0.2799 REMARK 3 T33: 0.2953 T12: -0.0237 REMARK 3 T13: -0.0036 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.3651 L22: 1.0524 REMARK 3 L33: 1.8675 L12: -0.3779 REMARK 3 L13: 0.1335 L23: -0.3999 REMARK 3 S TENSOR REMARK 3 S11: 0.0465 S12: 0.0381 S13: 0.0991 REMARK 3 S21: 0.0501 S22: -0.0773 S23: -0.0333 REMARK 3 S31: -0.2137 S32: -0.0084 S33: 0.0404 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 9V0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1300059585. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 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 : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12784 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 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 : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG3000 , 0.1 M TRIS PH 7.5 , 0.2 REMARK 280 M NACL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 24.71400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.75600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.44050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.75600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.71400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.44050 REMARK 290 SMTRY3 4 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: 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 ALA A 204 REMARK 465 SER A 205 REMARK 465 GLY A 206 REMARK 465 LYS A 207 REMARK 465 ASN A 208 REMARK 465 ARG A 209 REMARK 465 HIS A 210 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 ARG A 31 -43.43 73.11 REMARK 500 ALA A 55 70.42 -112.83 REMARK 500 ALA A 105 -164.74 58.03 REMARK 500 ARG A 180 72.89 -152.81 REMARK 500 ALA A 183 79.84 -155.14 REMARK 500 ASP A 229 24.99 46.38 REMARK 500 SER A 315 71.23 -69.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 9V0M A 1 363 UNP A0QTQ3 A0QTQ3_MYCS2 1 363 SEQADV 9V0M SER A -3 UNP A0QTQ3 EXPRESSION TAG SEQADV 9V0M PRO A -2 UNP A0QTQ3 EXPRESSION TAG SEQADV 9V0M GLU A -1 UNP A0QTQ3 EXPRESSION TAG SEQADV 9V0M PHE A 0 UNP A0QTQ3 EXPRESSION TAG SEQRES 1 A 367 SER PRO GLU PHE MET SER ALA PRO SER PHE VAL PHE ALA SEQRES 2 A 367 GLY PRO SER GLY VAL LEU ILE GLY GLU GLY VAL GLN THR SEQRES 3 A 367 GLY PHE ALA THR ILE ALA GLY ALA ARG ALA ALA LEU THR SEQRES 4 A 367 SER GLY ALA ALA ASP LEU VAL VAL GLY ALA LEU PRO PHE SEQRES 5 A 367 ASP LEU THR GLY PRO ALA ALA LEU HIS ALA PRO ALA SER SEQRES 6 A 367 ALA ARG VAL ALA GLY ALA LEU PRO ASP TRP PRO THR GLY SEQRES 7 A 367 THR PRO PRO VAL LEU ARG THR ARG GLU THR LEU PRO SER SEQRES 8 A 367 GLY ASP VAL HIS ARG GLU ARG VAL ALA GLU ALA VAL ARG SEQRES 9 A 367 ARG LEU ARG ASP ALA ASP THR PRO LEU ASP LYS VAL VAL SEQRES 10 A 367 LEU ALA ARG ALA LEU ARG LEU THR ALA GLU ALA PRO TRP SEQRES 11 A 367 ASP PRO ARG THR VAL LEU ARG ARG LEU ALA ASP ALA ASP SEQRES 12 A 367 PRO ALA ALA THR VAL TYR LEU ALA ASP LEU SER PRO ALA SEQRES 13 A 367 GLY ASP PRO HIS THR GLY THR VAL LEU VAL GLY ALA SER SEQRES 14 A 367 PRO GLU LEU LEU VAL ALA ARG ASP GLY ASP GLU VAL ILE SEQRES 15 A 367 CYS ARG PRO PHE ALA GLY SER ALA PRO ARG SER ALA ASP SEQRES 16 A 367 LEU GLU THR ASP ARG ALA ASN ALA ALA ALA LEU ALA ALA SEQRES 17 A 367 SER GLY LYS ASN ARG HIS GLU HIS GLU LEU VAL VAL ASP SEQRES 18 A 367 VAL MET ARG LYS ALA LEU ASP PRO LEU CYS VAL ASP LEU SEQRES 19 A 367 GLN ILE ALA ALA GLN PRO GLU LEU HIS ALA THR ASP ALA SEQRES 20 A 367 LEU TRP HIS LEU SER THR PRO ILE ARG GLY ARG LEU ARG SEQRES 21 A 367 ASP LYS ALA ILE THR ALA ILE ASP LEU ALA VAL ALA LEU SEQRES 22 A 367 HIS PRO THR PRO ALA VAL GLY GLY VAL PRO THR ASP LEU SEQRES 23 A 367 ALA ALA SER LEU ILE THR GLU LEU GLU GLY ASP ARG GLY SEQRES 24 A 367 PHE TYR ALA GLY ALA VAL GLY TRP CYS ASP SER ALA GLY SEQRES 25 A 367 ASN GLY ARG TRP VAL VAL SER ILE ARG CYS ALA VAL LEU SEQRES 26 A 367 SER ALA ASP ARG ARG VAL ALA LEU ALA ASN ALA GLY GLY SEQRES 27 A 367 GLY ILE VAL ALA GLU SER ASP PRO ASP ASP GLU VAL ASP SEQRES 28 A 367 GLU THR THR THR LYS PHE ARG THR ILE LEU THR GLY LEU SEQRES 29 A 367 GLY VAL GLN FORMUL 2 HOH *24(H2 O) HELIX 1 AA1 PRO A -2 ALA A 3 1 6 HELIX 2 AA2 ALA A 28 ALA A 33 1 6 HELIX 3 AA3 LEU A 34 GLY A 37 5 4 HELIX 4 AA4 SER A 87 ASP A 104 1 18 HELIX 5 AA5 ASP A 127 ASP A 139 1 13 HELIX 6 AA6 SER A 150 THR A 157 5 8 HELIX 7 AA7 ASP A 191 ALA A 203 1 13 HELIX 8 AA8 HIS A 212 ASP A 224 1 13 HELIX 9 AA9 THR A 261 HIS A 270 1 10 HELIX 10 AB1 PRO A 279 GLU A 291 1 13 HELIX 11 AB2 ASP A 341 PHE A 353 1 13 HELIX 12 AB3 PHE A 353 LEU A 360 1 8 SHEET 1 AA116 LEU A 79 LEU A 85 0 SHEET 2 AA116 LYS A 111 ALA A 122 -1 O ARG A 119 N GLU A 83 SHEET 3 AA116 VAL A 327 ILE A 336 -1 O ILE A 336 N VAL A 112 SHEET 4 AA116 CYS A 318 LEU A 321 -1 N VAL A 320 O LEU A 329 SHEET 5 AA116 VAL A 160 SER A 165 -1 N VAL A 160 O LEU A 321 SHEET 6 AA116 THR A 143 ASP A 148 -1 N ALA A 147 O LEU A 161 SHEET 7 AA116 PHE A 6 GLY A 10 -1 N ALA A 9 O VAL A 144 SHEET 8 AA116 GLY A 13 PHE A 24 -1 O LEU A 15 N PHE A 8 SHEET 9 AA116 ALA A 55 ALA A 65 -1 O LEU A 56 N PHE A 24 SHEET 10 AA116 LEU A 41 LEU A 46 -1 N ALA A 45 O ALA A 55 SHEET 11 AA116 ALA A 300 ASP A 305 -1 O ALA A 300 N LEU A 46 SHEET 12 AA116 GLY A 310 VAL A 314 -1 O VAL A 313 N VAL A 301 SHEET 13 AA116 LEU A 168 ASP A 173 -1 N ARG A 172 O GLY A 310 SHEET 14 AA116 GLU A 176 ARG A 180 -1 O GLU A 176 N ASP A 173 SHEET 15 AA116 ILE A 251 LEU A 255 -1 O ILE A 251 N CYS A 179 SHEET 16 AA116 CYS A 227 ILE A 232 -1 N GLN A 231 O ARG A 252 SHEET 1 AA2 3 LEU A 79 LEU A 85 0 SHEET 2 AA2 3 LYS A 111 ALA A 122 -1 O ARG A 119 N GLU A 83 SHEET 3 AA2 3 GLY A 277 VAL A 278 -1 O VAL A 278 N LYS A 111 SHEET 1 AA3 3 PHE A 182 PRO A 187 0 SHEET 2 AA3 3 LEU A 244 SER A 248 -1 O TRP A 245 N ALA A 186 SHEET 3 AA3 3 GLU A 237 ALA A 240 -1 N GLU A 237 O SER A 248 CISPEP 1 LEU A 85 PRO A 86 0 12.08 CISPEP 2 HIS A 270 PRO A 271 0 0.76 CISPEP 3 VAL A 278 PRO A 279 0 -9.89 CRYST1 49.428 60.881 121.512 90.00 90.00 90.00 P 21 21 21 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 0.020231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008230 0.00000 MASTER 243 0 0 12 22 0 0 6 2654 1 0 29 END