HEADER ISOMERASE 28-JUN-21 7R9B TITLE CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM CANDIDATUS TITLE 2 ROIZMANBACTERIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANDIDATUS ROIZMANBACTERIA; SOURCE 3 ORGANISM_TAXID: 1752723; SOURCE 4 GENE: A3B50_02135; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TIM, TRIOSEPHOSPHATE ISOMERASE, GLYCOLYSIS, GLUCONEOGENESIS, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.VICKERS,W.M.PATRICK,D.FRAGA REVDAT 2 18-OCT-23 7R9B 1 REMARK REVDAT 1 06-JUL-22 7R9B 0 JRNL AUTH C.J.VICKERS,W.M.PATRICK,D.FRAGA JRNL TITL CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM JRNL TITL 2 CANDIDATUS ROIZMANBACTERIA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 714 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 37.6100 - 3.7600 1.00 2825 161 0.1641 0.1906 REMARK 3 2 3.7600 - 2.9800 1.00 2757 145 0.1918 0.2624 REMARK 3 3 2.9800 - 2.6000 1.00 2783 102 0.2190 0.2580 REMARK 3 4 2.6000 - 2.3700 1.00 2715 152 0.2107 0.2634 REMARK 3 5 2.3700 - 2.2000 0.99 2678 154 0.2184 0.2890 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) : 0.257 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.124 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.92 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 1738 REMARK 3 ANGLE : 0.940 2365 REMARK 3 CHIRALITY : 0.056 272 REMARK 3 PLANARITY : 0.006 306 REMARK 3 DIHEDRAL : 13.265 231 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 7R9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000257823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-20 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14485 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 41.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 20.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 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: PHENIX REMARK 200 STARTING MODEL: 1YYA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE/CITRATE PH 4.2, 40% REMARK 280 V/V PEG 300., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 13.67167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.34333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.34333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.67167 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: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 163.40550 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 94.34221 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 13.67167 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 445 LIES ON A SPECIAL POSITION. 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 2 CG CD CE NZ REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 ASP A 33 CG OD1 OD2 REMARK 470 ARG A 36 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 109 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 113 CG CD OE1 OE2 REMARK 470 LYS A 139 CG CD CE NZ REMARK 470 GLU A 153 CG CD OE1 OE2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 GLU A 190 CG CD OE1 OE2 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 9 -138.83 50.35 REMARK 500 ALA A 10 57.72 -94.04 REMARK 500 LYS A 12 143.68 95.37 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7R9B A 1 223 UNP A0A1F7J4N7_9BACT DBREF2 7R9B A A0A1F7J4N7 1 223 SEQRES 1 A 223 MET LYS TYR ILE ILE ALA ASN TRP LYS ALA HIS LYS THR SEQRES 2 A 223 LEU GLU GLU ALA SER ALA TRP VAL ASP SER VAL ASN LYS SEQRES 3 A 223 GLN ILE SER GLN THR PRO ASP VAL GLN ARG LYS LEU GLU SEQRES 4 A 223 ASP ASP GLU LEU ILE ILE LEU ILE ALA ALA PRO PHE PRO SEQRES 5 A 223 PHE LEU VAL PRO LEU SER GLN LYS ILE SER GLN LYS ASN SEQRES 6 A 223 LEU ALA VAL ALA ALA GLN ASP VAL SER VAL TYR GLY GLU SEQRES 7 A 223 GLY ALA TYR THR GLY GLU VAL THR ALA LYS MET LEU LYS SEQRES 8 A 223 GLY VAL THR THR HIS VAL LEU ILE GLY HIS SER GLU ARG SEQRES 9 A 223 LYS ASP TYR PHE HIS GLU THR ASP GLU VAL VAL LEU LYS SEQRES 10 A 223 LYS SER GLU GLN VAL LEU SER GLN GLY LEU SER PRO ILE SEQRES 11 A 223 PHE CYS ILE GLN ASN GLU SER ASN LYS ILE PRO GLU GLY SEQRES 12 A 223 ALA ASN ILE ILE ALA TYR ASP PRO LYS GLU ALA ILE GLY SEQRES 13 A 223 THR GLY LYS ASN VAL PRO GLY GLU GLU THR ALA THR PHE SEQRES 14 A 223 ARG LYS LYS LEU ASN LEU PHE PRO ASP ALA VAL PHE LEU SEQRES 15 A 223 TYR GLY GLY SER VAL ASN PRO GLU SER ILE ASP GLU TYR SEQRES 16 A 223 LEU SER HIS PRO GLU ILE ASN GLY PHE LEU VAL GLY GLY SEQRES 17 A 223 SER SER LEU ASP PRO GLU GLU PHE PHE GLU LEU VAL LYS SEQRES 18 A 223 LYS LEU HET PO4 A 301 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *76(H2 O) HELIX 1 AA1 THR A 13 GLN A 30 1 18 HELIX 2 AA2 THR A 31 ASP A 40 1 10 HELIX 3 AA3 PRO A 50 PRO A 52 5 3 HELIX 4 AA4 PHE A 53 LYS A 60 1 8 HELIX 5 AA5 THR A 86 THR A 94 1 9 HELIX 6 AA6 HIS A 101 HIS A 109 1 9 HELIX 7 AA7 THR A 111 GLN A 125 1 15 HELIX 8 AA8 PRO A 151 ILE A 155 5 5 HELIX 9 AA9 PRO A 162 LYS A 172 1 11 HELIX 10 AB1 ILE A 192 SER A 197 1 6 HELIX 11 AB2 GLY A 207 LEU A 211 5 5 HELIX 12 AB3 ASP A 212 LYS A 222 1 11 SHEET 1 AA1 8 LEU A 66 ALA A 69 0 SHEET 2 AA1 8 LEU A 43 ALA A 48 1 N ILE A 47 O ALA A 69 SHEET 3 AA1 8 LYS A 2 ASN A 7 1 N ALA A 6 O LEU A 46 SHEET 4 AA1 8 GLY A 203 VAL A 206 1 O VAL A 206 N ASN A 7 SHEET 5 AA1 8 VAL A 180 GLY A 184 1 N TYR A 183 O LEU A 205 SHEET 6 AA1 8 ILE A 146 TYR A 149 1 N ILE A 147 O LEU A 182 SHEET 7 AA1 8 SER A 128 ILE A 133 1 N PHE A 131 O ILE A 146 SHEET 8 AA1 8 HIS A 96 ILE A 99 1 N VAL A 97 O ILE A 130 CRYST1 108.937 108.937 41.015 90.00 90.00 120.00 P 31 2 1 6 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 0.009180 0.005300 0.000000 0.00000 SCALE2 0.000000 0.010600 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024381 0.00000