HEADER OXIDOREDUCTASE 14-MAY-14 4ULX TITLE CRYSTAL STRUCTURE OF ANCESTRAL THIOREDOXIN, RELATIVE TO THE LAST TITLE 2 COMMON ANCESTOR OF THE CYANOBACTERIAL, DEINOCOCCUS AND THERMUS TITLE 3 GROUPS, LPBCA-L89K MUTANT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LPBCA-L89K THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 EC: 4.7.1.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET30A PLUS KEYWDS OXIDOREDUCTASE, ANCESTRAL EXPDTA X-RAY DIFFRACTION AUTHOR J.A.GAVIRA,V.A.RISSO,B.IBARRA-MOLERO,J.M.SANCHEZ-RUIZ REVDAT 3 10-JAN-24 4ULX 1 REMARK REVDAT 2 04-FEB-15 4ULX 1 JRNL REVDAT 1 26-NOV-14 4ULX 0 JRNL AUTH V.A.RISSO,F.MANSSOUR-TRIEDO,A.DELGADO-DELGADO,R.ARCO, JRNL AUTH 2 A.BARROSO-DELJESUS,A.INGLES-PRIETO,R.GODOY-RUIZ,J.A.GAVIRA, JRNL AUTH 3 E.A.GAUCHER,B.IBARRA-MOLERO,J.M.SANCHEZ-RUIZ JRNL TITL MUTATIONAL STUDIES ON RESURRECTED ANCESTRAL PROTEINS REVEAL JRNL TITL 2 CONSERVATION OF SITE-SPECIFIC AMINO ACID PREFERENCES JRNL TITL 3 THROUGHOUT EVOLUTIONARY HISTORY. JRNL REF MOL.BIOL.EVOL. V. 32 440 2015 JRNL REFN ISSN 0737-4038 JRNL PMID 25392342 JRNL DOI 10.1093/MOLBEV/MSU312 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 3756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 167 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 32.7971 - 2.3503 1.00 3589 167 0.1992 0.2437 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.10 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 : 0.003 899 REMARK 3 ANGLE : 0.737 1222 REMARK 3 CHIRALITY : 0.028 136 REMARK 3 PLANARITY : 0.005 161 REMARK 3 DIHEDRAL : 14.493 355 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 2 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8063 2.5719 -13.6359 REMARK 3 T TENSOR REMARK 3 T11: 0.2472 T22: 0.2120 REMARK 3 T33: 0.1782 T12: 0.0586 REMARK 3 T13: 0.0052 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 2.4827 L22: 3.6490 REMARK 3 L33: 2.0997 L12: 0.1136 REMARK 3 L13: 0.5859 L23: 0.5738 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: -0.0506 S13: -0.0938 REMARK 3 S21: 0.2183 S22: -0.0732 S23: -0.2421 REMARK 3 S31: 0.1457 S32: -0.0398 S33: 0.0429 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 48 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7740 7.1287 -17.7849 REMARK 3 T TENSOR REMARK 3 T11: 0.1649 T22: 0.2053 REMARK 3 T33: 0.1981 T12: -0.0710 REMARK 3 T13: -0.0490 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.9446 L22: 4.0453 REMARK 3 L33: 1.5125 L12: 0.3115 REMARK 3 L13: -0.6216 L23: -0.5727 REMARK 3 S TENSOR REMARK 3 S11: 0.0223 S12: -0.0299 S13: 0.1671 REMARK 3 S21: -0.5008 S22: -0.0597 S23: 0.2437 REMARK 3 S31: 0.1178 S32: 0.0686 S33: 0.0391 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 76 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.6777 11.4860 -11.6618 REMARK 3 T TENSOR REMARK 3 T11: 0.3384 T22: 0.1737 REMARK 3 T33: 0.3030 T12: 0.0071 REMARK 3 T13: -0.0953 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 2.0775 L22: 2.1088 REMARK 3 L33: 3.9947 L12: -1.2113 REMARK 3 L13: -0.8436 L23: -0.3085 REMARK 3 S TENSOR REMARK 3 S11: 0.1883 S12: -0.2325 S13: 0.6151 REMARK 3 S21: 0.1680 S22: -0.1031 S23: 0.4130 REMARK 3 S31: -0.5383 S32: -0.1618 S33: -0.1032 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 95 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7363 10.6909 -1.4223 REMARK 3 T TENSOR REMARK 3 T11: 0.5112 T22: 0.4004 REMARK 3 T33: 0.3914 T12: 0.0346 REMARK 3 T13: 0.1583 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 5.8404 L22: 5.5828 REMARK 3 L33: 3.4877 L12: 0.5009 REMARK 3 L13: -0.6616 L23: -0.1446 REMARK 3 S TENSOR REMARK 3 S11: 0.2930 S12: -0.0342 S13: 0.9165 REMARK 3 S21: 0.0327 S22: -0.1650 S23: -0.1005 REMARK 3 S31: -1.0613 S32: -0.9051 S33: -0.2626 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 4ULX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1290060618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 32.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.060 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: PDB ENTRY 2YJ7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: COUNTERDIFFUSION METHOD: 0.1M NA REMARK 280 ACETATE PH 4.0, 20% PEG 400, 15% PEG 4000 & 10% PEG 8000 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 17.58600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.52000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.44100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.52000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.58600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.44100 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 61 NZ LYS A 89 3544 2.18 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 TRP A 30 47.60 -98.13 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 CL A 1107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D27 RELATED DB: PDB REMARK 900 LIGAND BINDING REGIONS OF PSEUDOMONAS AERUGINOSA PAO1 AMINO ACID REMARK 900 CHEMORECEPTORS PCTA IN COMPLEX WITH L-TRP DBREF 4ULX A 1 106 PDB 4ULX 4ULX 1 106 SEQRES 1 A 106 MET SER VAL ILE GLU VAL THR ASP GLU ASN PHE GLU GLN SEQRES 2 A 106 GLU VAL LEU LYS SER ASP LYS PRO VAL LEU VAL ASP PHE SEQRES 3 A 106 TRP ALA PRO TRP CYS GLY PRO CYS ARG MET ILE ALA PRO SEQRES 4 A 106 ILE ILE GLU GLU LEU ALA LYS GLU TYR GLU GLY LYS VAL SEQRES 5 A 106 LYS VAL VAL LYS VAL ASN VAL ASP GLU ASN PRO ASN THR SEQRES 6 A 106 ALA ALA GLN TYR GLY ILE ARG SER ILE PRO THR LEU LEU SEQRES 7 A 106 LEU PHE LYS ASN GLY GLN VAL VAL ASP ARG LYS VAL GLY SEQRES 8 A 106 ALA GLN PRO LYS GLU ALA LEU LYS GLU ARG ILE ASP LYS SEQRES 9 A 106 HIS LEU HET CL A1107 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *16(H2 O) HELIX 1 1 ASN A 10 VAL A 15 1 6 HELIX 2 2 CYS A 31 TYR A 48 1 18 HELIX 3 3 ASN A 62 TYR A 69 1 8 HELIX 4 4 PRO A 94 LYS A 104 1 11 SHEET 1 AA 5 ILE A 4 VAL A 6 0 SHEET 2 AA 5 LYS A 53 ASN A 58 1 O VAL A 54 N ILE A 4 SHEET 3 AA 5 VAL A 22 TRP A 27 1 O LEU A 23 N VAL A 55 SHEET 4 AA 5 THR A 76 PHE A 80 -1 O THR A 76 N PHE A 26 SHEET 5 AA 5 VAL A 85 VAL A 90 -1 N VAL A 86 O LEU A 79 SSBOND 1 CYS A 31 CYS A 34 1555 1555 2.03 CISPEP 1 ILE A 74 PRO A 75 0 -0.72 SITE 1 AC1 4 TRP A 27 CYS A 34 ALA A 38 LYS A 56 CRYST1 35.172 38.882 61.040 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 0.028432 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025719 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016383 0.00000