HEADER HYDROLASE 29-JAN-16 5HWH TITLE STRUCTURE OF A CYSTEINE HYDROLASE WITH A POSITIVE SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCHORISMATASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROBACTERIUM HYDROCARBONOXYDANS; SOURCE 3 ORGANISM_TAXID: 273678; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HYDROLASE, CATALYIC TRIAD EXPDTA X-RAY DIFFRACTION AUTHOR Y.FENG,S.GAO REVDAT 3 20-MAR-24 5HWH 1 REMARK REVDAT 2 20-FEB-19 5HWH 1 SOURCE REVDAT 1 01-FEB-17 5HWH 0 JRNL AUTH S.GAO,Y.FENG JRNL TITL STRUCTURE OF A CYSTEINE HYDROLASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1355 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 24.7483 - 3.8533 0.62 2617 132 0.1816 0.2056 REMARK 3 2 3.8533 - 3.0603 0.62 2645 131 0.1691 0.2030 REMARK 3 3 3.0603 - 2.6740 0.70 2934 134 0.1959 0.2748 REMARK 3 4 2.6740 - 2.4297 0.69 2908 147 0.1895 0.2470 REMARK 3 5 2.4297 - 2.2557 0.66 2758 162 0.1887 0.2221 REMARK 3 6 2.2557 - 2.1228 0.62 2574 158 0.1841 0.2223 REMARK 3 7 2.1228 - 2.0165 0.55 2336 116 0.1842 0.1898 REMARK 3 8 2.0165 - 1.9288 0.52 2167 128 0.1814 0.1922 REMARK 3 9 1.9288 - 1.8545 0.52 2168 137 0.1853 0.2288 REMARK 3 10 1.8545 - 1.7906 0.52 2193 110 0.1968 0.2383 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1377 REMARK 3 ANGLE : 1.060 1882 REMARK 3 CHIRALITY : 0.046 218 REMARK 3 PLANARITY : 0.005 246 REMARK 3 DIHEDRAL : 13.091 480 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 5HWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000217858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-15 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 : SSRF REMARK 200 BEAMLINE : BL17U 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26655 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL 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 (%): 58.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, SODIUM MALONATE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 29.05300 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 58.10600 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 58.10600 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 29.05300 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: 3270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 456 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 473 LIES ON A SPECIAL POSITION. 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 MET A -8 REMARK 465 GLY A -7 REMARK 465 SER A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 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 GLU A 95 CG CD OE1 OE2 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 OE2 GLU A 25 O HOH A 301 2.04 REMARK 500 O HOH A 302 O HOH A 421 2.08 REMARK 500 NH2 ARG A 69 O HOH A 302 2.13 REMARK 500 O HOH A 476 O HOH A 521 2.15 REMARK 500 O HOH A 476 O HOH A 535 2.15 REMARK 500 O HOH A 384 O HOH A 525 2.15 REMARK 500 O HOH A 479 O HOH A 518 2.17 REMARK 500 O HOH A 384 O HOH A 501 2.19 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 PHE A 110 -88.65 -122.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 66Z A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5HWG RELATED DB: PDB DBREF1 5HWH A 1 178 UNP A0A0K0XHU0_9MICO DBREF2 5HWH A A0A0K0XHU0 1 178 SEQADV 5HWH MET A -8 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH GLY A -7 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH SER A -6 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A -5 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A -4 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A -3 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A -2 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A -1 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH HIS A 0 UNP A0A0K0XHU EXPRESSION TAG SEQADV 5HWH ALA A 111 UNP A0A0K0XHU CYS 111 ENGINEERED MUTATION SEQRES 1 A 187 MET GLY SER HIS HIS HIS HIS HIS HIS MET ALA ALA PRO SEQRES 2 A 187 ARG ARG THR VAL VAL LEU ALA ILE ASP LEU GLN ALA GLY SEQRES 3 A 187 VAL THR PRO GLY CYS PHE ASP GLU GLU GLY VAL LEU SER SEQRES 4 A 187 ARG ALA ALA ALA LEU VAL GLU ARG ALA ARG ALA GLY GLY SEQRES 5 A 187 VAL PRO VAL VAL TRP VAL HIS HIS ASP PRO VAL GLY VAL SEQRES 6 A 187 GLY THR PRO GLU TRP GLU LEU ALA ALA PRO LEU HIS ARG SEQRES 7 A 187 ALA GLU GLY GLU PRO LEU VAL ARG LYS ASN TYR ARG ASP SEQRES 8 A 187 SER PHE ALA ASP THR THR LEU ARG GLU THR LEU ASP GLU SEQRES 9 A 187 LEU GLY ALA THR HIS LEU VAL ILE THR GLY ALA GLN SER SEQRES 10 A 187 ASP PHE ALA VAL ARG THR THR MET GLN ARG ALA ALA ALA SEQRES 11 A 187 GLU GLY TYR ASP VAL THR LEU VAL SER ASP ALA HIS THR SEQRES 12 A 187 THR VAL ASP THR GLU TRP GLU GLY VAL ARG ILE SER GLY SEQRES 13 A 187 GLU GLN ILE VAL ALA HIS THR ASN MET TYR PHE SER GLY SEQRES 14 A 187 LEU ARG TYR PRO GLY GLN GLU PHE VAL ILE ALA THR HIS SEQRES 15 A 187 ASP HIS VAL ALA LEU HET 66Z A 201 15 HETNAM 66Z (1~{S},4~{R})-3-AZABICYCLO[2.2.1]HEPT-5-EN-2-ONE FORMUL 2 66Z C6 H7 N O FORMUL 3 HOH *237(H2 O) HELIX 1 AA1 ASP A 24 GLY A 42 1 19 HELIX 2 AA2 PRO A 53 GLY A 55 5 3 HELIX 3 AA3 THR A 58 GLU A 62 5 5 HELIX 4 AA4 THR A 88 LEU A 96 1 9 HELIX 5 AA5 PHE A 110 GLY A 123 1 14 HELIX 6 AA6 SER A 146 GLY A 160 1 15 SHEET 1 AA1 6 LEU A 75 LYS A 78 0 SHEET 2 AA1 6 VAL A 46 HIS A 51 1 N TRP A 48 O VAL A 76 SHEET 3 AA1 6 THR A 7 ILE A 12 1 N VAL A 9 O VAL A 47 SHEET 4 AA1 6 HIS A 100 ALA A 106 1 O VAL A 102 N LEU A 10 SHEET 5 AA1 6 ASP A 125 THR A 134 1 O THR A 127 N ILE A 103 SHEET 6 AA1 6 PHE A 168 ALA A 171 1 O ALA A 171 N LEU A 128 SHEET 1 AA2 2 THR A 138 TRP A 140 0 SHEET 2 AA2 2 VAL A 143 ILE A 145 -1 O ILE A 145 N THR A 138 CISPEP 1 ALA A 65 PRO A 66 0 8.00 CISPEP 2 ALA A 106 GLN A 107 0 -10.50 SITE 1 AC1 7 ASP A 13 HIS A 51 ALA A 106 GLN A 107 SITE 2 AC1 7 PHE A 110 ALA A 111 HOH A 407 CRYST1 69.427 69.427 87.159 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 0.014404 0.008316 0.000000 0.00000 SCALE2 0.000000 0.016632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011473 0.00000