HEADER METAL BINDING PROTEIN 07-JAN-23 8HZ1 TITLE AMBIENT TEMPERATURE CRYSTAL STRUCTURE OF ESCHERICHIA COLI CYAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-SULFUR CLUSTER ASSEMBLY PROTEIN CYAY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYAY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS CYAY, ESCHERICHIA COLI, FRATAXIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.SHAFIEI,H.DEMIRCI REVDAT 1 25-JAN-23 8HZ1 0 JRNL AUTH A.SHAFIEI,H.DEMIRCI JRNL TITL AMBIENT TEMPERATURE CRYSTAL STRUCTURE OF ESCHERICHIA COLI JRNL TITL 2 CYAY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 7996 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.320 REMARK 3 R VALUE (WORKING SET) : 0.316 REMARK 3 FREE R VALUE : 0.356 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.890 REMARK 3 FREE R VALUE TEST SET COUNT : 791 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 30.9400 - 3.6400 1.00 1379 147 0.2526 0.2786 REMARK 3 2 3.6300 - 2.8800 1.00 1292 144 0.2950 0.3647 REMARK 3 3 2.8800 - 2.5200 0.99 1248 140 0.3528 0.3715 REMARK 3 4 2.5200 - 2.2900 0.96 1228 133 0.3555 0.4267 REMARK 3 5 2.2900 - 2.1300 0.86 1080 121 0.3971 0.4070 REMARK 3 6 2.1200 - 2.0000 0.78 978 106 0.4250 0.4288 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) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 44.820 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 : 0.002 NULL REMARK 3 ANGLE : 0.448 NULL REMARK 3 CHIRALITY : 0.043 125 REMARK 3 PLANARITY : 0.004 159 REMARK 3 DIHEDRAL : 5.050 112 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1987 -12.6081 0.6828 REMARK 3 T TENSOR REMARK 3 T11: 0.1788 T22: 0.1711 REMARK 3 T33: 0.3808 T12: 0.0149 REMARK 3 T13: 0.0133 T23: 0.0161 REMARK 3 L TENSOR REMARK 3 L11: 2.2324 L22: 2.0089 REMARK 3 L33: 1.2459 L12: -0.1765 REMARK 3 L13: -0.4402 L23: 0.3295 REMARK 3 S TENSOR REMARK 3 S11: 0.1029 S12: -0.0516 S13: -0.0830 REMARK 3 S21: 0.1170 S22: -0.2316 S23: -0.1190 REMARK 3 S31: 0.0421 S32: 0.0644 S33: -0.0125 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8747 -16.5197 14.7440 REMARK 3 T TENSOR REMARK 3 T11: -0.1405 T22: 0.1233 REMARK 3 T33: 0.1000 T12: 0.1205 REMARK 3 T13: 0.2025 T23: -0.1546 REMARK 3 L TENSOR REMARK 3 L11: 1.3312 L22: 0.5298 REMARK 3 L33: 0.6399 L12: -0.4611 REMARK 3 L13: -0.5163 L23: 0.1975 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.2009 S13: 0.1601 REMARK 3 S21: 0.0811 S22: 0.0640 S23: 0.0821 REMARK 3 S31: -0.0350 S32: 0.0634 S33: -0.1017 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0415 -22.8877 1.0392 REMARK 3 T TENSOR REMARK 3 T11: 0.0575 T22: 0.1464 REMARK 3 T33: 0.0691 T12: 0.0071 REMARK 3 T13: -0.0527 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.9248 L22: 1.5250 REMARK 3 L33: 1.8509 L12: -0.1833 REMARK 3 L13: -0.6555 L23: 0.5977 REMARK 3 S TENSOR REMARK 3 S11: 0.1182 S12: 0.0879 S13: -0.0917 REMARK 3 S21: -0.3994 S22: 0.0393 S23: 0.0472 REMARK 3 S31: 0.0274 S32: -0.2159 S33: 0.1325 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.7228 -14.9526 1.3208 REMARK 3 T TENSOR REMARK 3 T11: 0.1372 T22: 0.1758 REMARK 3 T33: 0.1782 T12: 0.0628 REMARK 3 T13: 0.0028 T23: 0.0542 REMARK 3 L TENSOR REMARK 3 L11: 1.3780 L22: 0.9044 REMARK 3 L33: 3.1880 L12: -0.4608 REMARK 3 L13: -0.4325 L23: 0.4600 REMARK 3 S TENSOR REMARK 3 S11: -0.1640 S12: 0.2374 S13: 0.0598 REMARK 3 S21: 0.0527 S22: -0.0536 S23: -0.0255 REMARK 3 S31: -0.0042 S32: 0.0383 S33: 0.0608 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 8HZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034626. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU PHOTONJET-R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO 1.171.42.35A REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO 1.171.42.35A REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7996 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 31.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 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: PHASER 2.8.3 REMARK 200 STARTING MODEL: 1EW4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID, 4.0 M SODIUM REMARK 280 CHLORIDE (PH 4.0), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 67.41933 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 33.70967 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 33.70967 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 67.41933 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 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 OG SER A 104 O HOH A 201 2.10 REMARK 500 NH1 ARG A 53 O HOH A 202 2.17 REMARK 500 OD2 ASP A 3 O HOH A 203 2.18 REMARK 500 NZ LYS A 65 O HOH A 204 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 ASP A 81 5.19 -69.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HZ1 A 1 106 UNP C3SKF0 C3SKF0_ECOLX 1 106 SEQRES 1 A 106 MET ASN ASP SER GLU PHE HIS ARG LEU ALA ASP GLN LEU SEQRES 2 A 106 TRP LEU THR ILE GLU GLU ARG LEU ASP ASP TRP ASP GLY SEQRES 3 A 106 ASP SER ASP ILE ASP CYS GLU ILE ASN GLY GLY VAL LEU SEQRES 4 A 106 THR ILE THR PHE GLU ASN GLY SER LYS ILE ILE ILE ASN SEQRES 5 A 106 ARG GLN GLU PRO LEU HIS GLN VAL TRP LEU ALA THR LYS SEQRES 6 A 106 GLN GLY GLY TYR HIS PHE ASP LEU LYS GLY ASP GLU TRP SEQRES 7 A 106 ILE CYS ASP ARG SER GLY GLU THR PHE TRP ASP LEU LEU SEQRES 8 A 106 GLU GLN ALA ALA THR GLN GLN ALA GLY GLU THR VAL SER SEQRES 9 A 106 PHE ARG FORMUL 2 HOH *43(H2 O) HELIX 1 AA1 ASN A 2 TRP A 24 1 23 HELIX 2 AA2 THR A 86 GLY A 100 1 15 SHEET 1 AA1 6 ILE A 30 ASN A 35 0 SHEET 2 AA1 6 VAL A 38 PHE A 43 -1 O THR A 40 N GLU A 33 SHEET 3 AA1 6 LYS A 48 GLN A 54 -1 O ILE A 51 N LEU A 39 SHEET 4 AA1 6 GLN A 59 ALA A 63 -1 O GLN A 59 N GLN A 54 SHEET 5 AA1 6 GLY A 68 LYS A 74 -1 O TYR A 69 N LEU A 62 SHEET 6 AA1 6 GLU A 77 CYS A 80 -1 O GLU A 77 N LYS A 74 CRYST1 45.167 45.167 101.129 90.00 90.00 120.00 P 32 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 0.022140 0.012783 0.000000 0.00000 SCALE2 0.000000 0.025565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009888 0.00000