HEADER HYDROLASE 02-JAN-24 8RL0 TITLE CRYSTAL STRUCTURE OF A CYSTEINE HYDROLASE FROM USTILAGO MAYDIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCHORISMATASE-LIKE DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: USTILAGO MAYDIS 521; SOURCE 3 ORGANISM_TAXID: 237631; SOURCE 4 GENE: UMAG_12021; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS USTILAGO MAYDIS, CYSTEINE HYDROLASE, BIOTROPHY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.ALTEGOER,M.CHRIST,G.BANGE REVDAT 1 15-JAN-25 8RL0 0 JRNL AUTH I.RUBIO ELIZALDE,M.CHRIST,P.WEILAND,E.JALOMO,L.VOLL, JRNL AUTH 2 F.ALTEGOER,G.BANGE JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF AN JRNL TITL 2 ISOCHORISMATE (ISC)-LIKE PROTEIN IN A PLANT-PATHOGENIC JRNL TITL 3 FUNGUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16971 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 848 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 42.1500 - 3.2800 1.00 2880 152 0.1737 0.2110 REMARK 3 2 3.2800 - 2.6100 1.00 2727 144 0.2287 0.2847 REMARK 3 3 2.6100 - 2.2800 1.00 2680 141 0.2308 0.2760 REMARK 3 4 2.2800 - 2.0700 1.00 2664 140 0.2712 0.3002 REMARK 3 5 2.0700 - 1.9200 1.00 2651 139 0.3388 0.3833 REMARK 3 6 1.9200 - 1.8100 0.97 2550 134 0.4315 0.4280 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) : 0.247 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.411 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.16 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 : 0.006 1592 REMARK 3 ANGLE : 0.842 2153 REMARK 3 CHIRALITY : 0.053 265 REMARK 3 PLANARITY : 0.006 272 REMARK 3 DIHEDRAL : 6.032 210 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 8RL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292122046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-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 : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976253 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16972 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 42.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.13540 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.84200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 32.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 7.0, 20% PEG-2000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.12500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.12500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.12500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.12500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.12500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.12500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.12500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.12500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 -1.000000 0.000000 0.000000 94.25000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 47.12500 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -47.12500 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 47.12500 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 47.12500 REMARK 350 BIOMT3 4 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 MET A -14 REMARK 465 GLY A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 ALA A -6 REMARK 465 ALA A -5 REMARK 465 ALA A -4 REMARK 465 ALA A -3 REMARK 465 PHE A -2 REMARK 465 ALA A 203 REMARK 465 LYS A 204 REMARK 465 TYR A 205 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 OD1 ASP A 44 O HOH A 301 1.92 REMARK 500 OE1 GLU A 151 O HOH A 302 2.19 REMARK 500 OE1 GLN A 169 O HOH A 303 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 PRO A 72 160.47 -46.53 REMARK 500 VAL A 115 -88.13 -121.93 REMARK 500 VAL A 172 -39.29 71.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8RKZ RELATED DB: PDB REMARK 900 8RKZ CONTAINS A HOMOLOG OF THE PROTEIN DBREF1 8RL0 A -6 205 UNP A0A0D1DWT4_USTMA DBREF2 8RL0 A A0A0D1DWT4 2 213 SEQADV 8RL0 MET A -14 UNP A0A0D1DWT INITIATING METHIONINE SEQADV 8RL0 GLY A -13 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -12 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -11 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -10 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -9 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -8 UNP A0A0D1DWT EXPRESSION TAG SEQADV 8RL0 HIS A -7 UNP A0A0D1DWT EXPRESSION TAG SEQRES 1 A 220 MET GLY HIS HIS HIS HIS HIS HIS ALA ALA ALA ALA PHE SEQRES 2 A 220 ARG THR ALA ARG ILE GLU LEU ALA LYS THR ALA PHE PHE SEQRES 3 A 220 LEU CYS ASP MET GLN GLU ARG PHE LYS THR VAL ILE SER SEQRES 4 A 220 ASN PHE ASP LEU ILE THR GLN THR SER ALA ARG MET LEU SEQRES 5 A 220 LYS ALA ALA LYS ILE LEU ASP VAL PRO VAL PHE THR THR SEQRES 6 A 220 GLU GLN ASN PRO LYS ALA LEU GLY ALA THR VAL SER PRO SEQRES 7 A 220 LEU SER ASP LEU LEU LYS ASP LEU PRO GLN ILE SER ALA SEQRES 8 A 220 ALA ALA VAL HIS PRO LYS THR LYS PHE SER MET ASP LEU SEQRES 9 A 220 PRO ASP ILE THR ASP LYS TRP LEU GLN SER ALA GLY ASP SEQRES 10 A 220 ILE LYS HIS VAL VAL ILE PHE GLY ILE GLU SER HIS VAL SEQRES 11 A 220 CYS VAL LEU GLN THR THR LEU ASP LEU LEU ASP ARG GLY SEQRES 12 A 220 ILE GLN VAL HIS VAL ILE LYS ASP GLY VAL SER SER CYS SEQRES 13 A 220 ASN VAL GLY GLU ILE ASP VAL ALA LEU GLU ARG MET ARG SEQRES 14 A 220 ASN SER GLY ALA GLN ILE THR THR SER GLU SER VAL LEU SEQRES 15 A 220 PHE GLN MET LEU VAL ASP ALA SER HIS PRO LYS PHE LYS SEQRES 16 A 220 ALA ILE SER GLY LEU ILE LYS GLU GLU LYS GLN GLN ILE SEQRES 17 A 220 LYS ASP ALA VAL ASN THR LEU GLY LEU ALA LYS TYR FORMUL 2 HOH *44(H2 O) HELIX 1 AA1 GLU A 4 ALA A 6 5 3 HELIX 2 AA2 GLN A 16 THR A 21 5 6 HELIX 3 AA3 ASN A 25 ASP A 44 1 20 HELIX 4 AA4 ASN A 53 GLY A 58 1 6 HELIX 5 AA5 PRO A 63 ASP A 70 1 8 HELIX 6 AA6 PRO A 72 ALA A 77 1 6 HELIX 7 AA7 ILE A 92 GLY A 101 1 10 HELIX 8 AA8 VAL A 115 ASP A 126 1 12 HELIX 9 AA9 ASN A 142 GLY A 144 5 3 HELIX 10 AB1 GLU A 145 SER A 156 1 12 HELIX 11 AB2 THR A 162 VAL A 172 1 11 HELIX 12 AB3 LYS A 178 GLU A 189 1 12 HELIX 13 AB4 GLU A 189 GLY A 201 1 13 SHEET 1 AA1 6 VAL A 79 LYS A 82 0 SHEET 2 AA1 6 VAL A 47 GLN A 52 1 N THR A 49 O HIS A 80 SHEET 3 AA1 6 THR A 8 CYS A 13 1 N LEU A 12 O PHE A 48 SHEET 4 AA1 6 HIS A 105 ILE A 111 1 O PHE A 109 N CYS A 13 SHEET 5 AA1 6 GLN A 130 SER A 139 1 O HIS A 132 N VAL A 106 SHEET 6 AA1 6 GLN A 159 THR A 161 1 O THR A 161 N LYS A 135 CISPEP 1 SER A 62 PRO A 63 0 -0.03 CISPEP 2 ILE A 111 GLU A 112 0 -14.26 CRYST1 94.250 94.250 40.030 90.00 90.00 90.00 P 4 21 2 8 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 0.010610 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024981 0.00000 MASTER 281 0 0 13 6 0 0 6 1614 1 0 17 END