HEADER SIGNALING PROTEIN 06-MAY-11 3RVK TITLE STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89: TITLE 2 N59D E89Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHEMOTAXIS PROTEIN CHEY; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B1882, CHEY, JW1871; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28ACHEYN59DE89Q KEYWDS TWO-COMPONENT, SIGNAL TRANSDUCTION, RESPONSE REGULATOR, CHEY, BETA- KEYWDS 2 ALPHA PROTEIN, CHEMOTAXIS, CHEZ, CHEX, CHEA, PHOSPHORYLATION, KEYWDS 3 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.M.IMMORMINO,C.A.STARBIRD,R.E.SILVERSMITH,R.B.BOURRET REVDAT 3 13-SEP-23 3RVK 1 REMARK SEQADV REVDAT 2 21-SEP-16 3RVK 1 JRNL REVDAT 1 09-MAY-12 3RVK 0 JRNL AUTH R.M.IMMORMINO,C.A.STARBIRD,R.E.SILVERSMITH,R.B.BOURRET JRNL TITL PROBING MECHANISTIC SIMILARITIES BETWEEN RESPONSE REGULATOR JRNL TITL 2 SIGNALING PROTEINS AND HALOACID DEHALOGENASE PHOSPHATASES. JRNL REF BIOCHEMISTRY V. 54 3514 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 25928369 JRNL DOI 10.1021/ACS.BIOCHEM.5B00286 REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 38086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1909 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 27.8288 - 2.7955 1.00 2900 159 0.1410 0.1562 REMARK 3 2 2.7955 - 2.2192 1.00 2789 137 0.1164 0.1406 REMARK 3 3 2.2192 - 1.9387 1.00 2768 126 0.1083 0.1399 REMARK 3 4 1.9387 - 1.7615 1.00 2731 138 0.1131 0.1556 REMARK 3 5 1.7615 - 1.6353 0.99 2691 139 0.1115 0.1565 REMARK 3 6 1.6353 - 1.5389 0.99 2703 146 0.1069 0.1205 REMARK 3 7 1.5389 - 1.4618 0.98 2617 152 0.1089 0.1615 REMARK 3 8 1.4618 - 1.3982 0.97 2674 123 0.1198 0.1522 REMARK 3 9 1.3982 - 1.3444 0.96 2568 144 0.1237 0.1482 REMARK 3 10 1.3444 - 1.2980 0.96 2558 126 0.1377 0.1599 REMARK 3 11 1.2980 - 1.2574 0.95 2519 161 0.1694 0.1934 REMARK 3 12 1.2574 - 1.2214 0.91 2476 118 0.1961 0.2452 REMARK 3 13 1.2214 - 1.1893 0.86 2283 147 0.2488 0.2766 REMARK 3 14 1.1893 - 1.1603 0.71 1900 93 0.2793 0.3341 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.30 REMARK 3 SHRINKAGE RADIUS : 0.05 REMARK 3 K_SOL : 0.50 REMARK 3 B_SOL : 90.21 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.57990 REMARK 3 B22 (A**2) : 1.66750 REMARK 3 B33 (A**2) : -1.08760 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1106 REMARK 3 ANGLE : 1.216 1507 REMARK 3 CHIRALITY : 0.068 169 REMARK 3 PLANARITY : 0.005 198 REMARK 3 DIHEDRAL : 11.992 450 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 3RVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1000065429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SAGITAL CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39493 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39900 REMARK 200 FOR SHELL : 2.100 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 3CHY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000 31% (W/V), NA CACODYLATE REMARK 280 100MM, PH 6.0, CALCIUM ACETATE 140MM, GLYCEROL 10% (V/V), 8.8 MG/ REMARK 280 ML CHEY, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 22.55850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.96300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.39300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 26.96300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.55850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.39300 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 O HOH A 247 O HOH A 315 4555 2.08 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 ASN A 62 -57.37 76.35 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 MN A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FQW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVATED CHEY REMARK 900 RELATED ID: 3RVJ RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVL RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVM RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVN RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVO RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVP RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-BEF3 COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVQ RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY-MN2+ COMPLEX WITH SUBSTITUTIONS AT 59 AND 89 REMARK 900 RELATED ID: 3RVR RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY N59D/E89R MOLYBDATE COMPLEX REMARK 900 RELATED ID: 3RVS RELATED DB: PDB REMARK 900 STRUCTURE OF THE CHEY N59D/E89R TUNGSTATE COMPLEX DBREF 3RVK A 1 129 UNP P0AE67 CHEY_ECOLI 1 129 SEQADV 3RVK GLY A -2 UNP P0AE67 EXPRESSION TAG SEQADV 3RVK SER A -1 UNP P0AE67 EXPRESSION TAG SEQADV 3RVK HIS A 0 UNP P0AE67 EXPRESSION TAG SEQADV 3RVK ASP A 59 UNP P0AE67 ASN 59 ENGINEERED MUTATION SEQADV 3RVK GLN A 89 UNP P0AE67 GLU 89 ENGINEERED MUTATION SEQRES 1 A 132 GLY SER HIS MET ALA ASP LYS GLU LEU LYS PHE LEU VAL SEQRES 2 A 132 VAL ASP ASP PHE SER THR MET ARG ARG ILE VAL ARG ASN SEQRES 3 A 132 LEU LEU LYS GLU LEU GLY PHE ASN ASN VAL GLU GLU ALA SEQRES 4 A 132 GLU ASP GLY VAL ASP ALA LEU ASN LYS LEU GLN ALA GLY SEQRES 5 A 132 GLY TYR GLY PHE VAL ILE SER ASP TRP ASP MET PRO ASN SEQRES 6 A 132 MET ASP GLY LEU GLU LEU LEU LYS THR ILE ARG ALA ASP SEQRES 7 A 132 GLY ALA MET SER ALA LEU PRO VAL LEU MET VAL THR ALA SEQRES 8 A 132 GLN ALA LYS LYS GLU ASN ILE ILE ALA ALA ALA GLN ALA SEQRES 9 A 132 GLY ALA SER GLY TYR VAL VAL LYS PRO PHE THR ALA ALA SEQRES 10 A 132 THR LEU GLU GLU LYS LEU ASN LYS ILE PHE GLU LYS LEU SEQRES 11 A 132 GLY MET HET MN A 130 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN MN 2+ FORMUL 3 HOH *262(H2 O) HELIX 1 1 PHE A 14 GLY A 29 1 16 HELIX 2 2 ASP A 38 ALA A 48 1 11 HELIX 3 3 ASP A 64 ASP A 75 1 12 HELIX 4 4 LYS A 91 ALA A 101 1 11 HELIX 5 5 THR A 112 GLY A 128 1 17 SHEET 1 A 5 VAL A 33 ALA A 36 0 SHEET 2 A 5 PHE A 8 VAL A 11 1 N VAL A 10 O GLU A 34 SHEET 3 A 5 PHE A 53 ASP A 57 1 O ILE A 55 N VAL A 11 SHEET 4 A 5 VAL A 83 THR A 87 1 O LEU A 84 N VAL A 54 SHEET 5 A 5 GLY A 105 VAL A 108 1 O GLY A 105 N MET A 85 CISPEP 1 LYS A 109 PRO A 110 0 -4.15 CISPEP 2 LYS A 109 PRO A 110 0 -2.43 SITE 1 AC1 7 ASP A 13 ASP A 57 ASP A 59 HOH A 136 SITE 2 AC1 7 HOH A 137 HOH A 138 HOH A 249 CRYST1 45.117 46.786 53.926 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 0.022165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018544 0.00000