HEADER STRUCTURAL PROTEIN 09-JUN-09 3HRA TITLE CRYSTAL STRUCTURE OF EF0377 AN ANKYRIN REPEAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANKYRIN REPEAT FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECALIS; SOURCE 3 ORGANISM_TAXID: 1351; SOURCE 4 STRAIN: V583; SOURCE 5 GENE: EF0377; 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: PQE10 KEYWDS ANKYRIN REPEAT, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.W.ISAACS,T.J.MITCHELL,A.RIBOLDI-TUNNICLIFFE REVDAT 2 01-NOV-23 3HRA 1 REMARK REVDAT 1 16-JUN-10 3HRA 0 JRNL AUTH N.W.ISAACS,T.J.MITCHELL,C.J.BENT,A.RIBOLDI-TUNNICLIFFE JRNL TITL CRYSTAL STRUCTURE OF EF0377 AN ANKYRIN REPEAT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.69 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) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.870 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 3 NUMBER OF REFLECTIONS : 16577 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 844 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 31.5560 - 3.0750 0.99 3291 174 0.1570 0.1770 REMARK 3 2 3.0750 - 2.4410 0.98 3087 155 0.1600 0.2160 REMARK 3 3 2.4410 - 2.1330 0.94 2949 168 0.1460 0.2030 REMARK 3 4 2.1330 - 1.9380 0.88 2710 154 0.1460 0.2160 REMARK 3 5 1.9380 - 1.7990 0.78 2417 120 0.1580 0.2080 REMARK 3 6 1.7990 - 1.6930 0.42 1279 73 0.1730 0.2430 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 : 0.42 REMARK 3 B_SOL : 46.77 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.07800 REMARK 3 B22 (A**2) : -0.16400 REMARK 3 B33 (A**2) : -1.91400 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 : 0.008 1574 REMARK 3 ANGLE : 1.026 2131 REMARK 3 CHIRALITY : 0.074 239 REMARK 3 PLANARITY : 0.004 287 REMARK 3 DIHEDRAL : 16.922 579 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -7.9555 6.4953 -9.4444 REMARK 3 T TENSOR REMARK 3 T11: 0.0032 T22: 0.0110 REMARK 3 T33: 0.0067 T12: 0.0013 REMARK 3 T13: 0.0054 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.4215 L22: 0.5062 REMARK 3 L33: 0.3978 L12: 0.2520 REMARK 3 L13: -0.3311 L23: -0.4001 REMARK 3 S TENSOR REMARK 3 S11: -0.0049 S12: -0.0401 S13: 0.0369 REMARK 3 S21: 0.0247 S22: -0.0060 S23: -0.0060 REMARK 3 S31: -0.0078 S32: 0.0235 S33: 0.0062 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 3HRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053486. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9755 REMARK 200 MONOCHROMATOR : LIQ. N2 COOLED SI-111 DOUBLE REMARK 200 CRYSTAL OR SI-111 CHANNEL CUT REMARK 200 MONOCHROMATORS (IN SERIES) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 31.551 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12700 REMARK 200 FOR THE DATA SET : 3.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 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: PHENIX REMARK 200 STARTING MODEL: 1NFI CHAIN E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4K, 100MM TRIS, 200MM SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 13.48050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.47950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.45100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.47950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.48050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.45100 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 465 LYS A 2 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 O HOH A 225 O HOH A 231 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 ASN A 108 -158.07 -105.78 REMARK 500 ASP A 128 38.37 -141.61 REMARK 500 ARG A 130 -15.84 81.46 REMARK 500 ARG A 151 -169.03 -119.89 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 202 DBREF 3HRA A 1 201 UNP Q838Q8 Q838Q8_ENTFA 1 201 SEQRES 1 A 201 MET LYS THR TYR GLU VAL GLY ALA LEU LEU GLU ALA ALA SEQRES 2 A 201 ASN GLN ARG ASP THR LYS LYS VAL LYS GLU ILE LEU GLN SEQRES 3 A 201 ASP THR THR TYR GLN VAL ASP GLU VAL ASP THR GLU GLY SEQRES 4 A 201 ASN THR PRO LEU ASN ILE ALA VAL HIS ASN ASN ASP ILE SEQRES 5 A 201 GLU ILE ALA LYS ALA LEU ILE ASP ARG GLY ALA ASP ILE SEQRES 6 A 201 ASN LEU GLN ASN SER ILE SER ASP SER PRO TYR LEU TYR SEQRES 7 A 201 ALA GLY ALA GLN GLY ARG THR GLU ILE LEU ALA TYR MET SEQRES 8 A 201 LEU LYS HIS ALA THR PRO ASP LEU ASN LYS HIS ASN ARG SEQRES 9 A 201 TYR GLY GLY ASN ALA LEU ILE PRO ALA ALA GLU LYS GLY SEQRES 10 A 201 HIS ILE ASP ASN VAL LYS LEU LEU LEU GLU ASP GLY ARG SEQRES 11 A 201 GLU ASP ILE ASP PHE GLN ASN ASP PHE GLY TYR THR ALA SEQRES 12 A 201 LEU ILE GLU ALA VAL GLY LEU ARG GLU GLY ASN GLN LEU SEQRES 13 A 201 TYR GLN ASP ILE VAL LYS LEU LEU MET GLU ASN GLY ALA SEQRES 14 A 201 ASP GLN SER ILE LYS ASP ASN SER GLY ARG THR ALA MET SEQRES 15 A 201 ASP TYR ALA ASN GLN LYS GLY TYR THR GLU ILE SER LYS SEQRES 16 A 201 ILE LEU ALA GLN TYR ASN HET CL A 202 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *247(H2 O) HELIX 1 1 GLY A 7 GLN A 15 1 9 HELIX 2 2 ASP A 17 GLN A 26 1 10 HELIX 3 3 THR A 41 ASN A 50 1 10 HELIX 4 4 ASP A 51 ARG A 61 1 11 HELIX 5 5 SER A 74 GLN A 82 1 9 HELIX 6 6 ARG A 84 ALA A 95 1 12 HELIX 7 7 ALA A 109 LYS A 116 1 8 HELIX 8 8 HIS A 118 GLY A 129 1 12 HELIX 9 9 THR A 142 LEU A 150 1 9 HELIX 10 10 ASN A 154 ASN A 167 1 14 HELIX 11 11 THR A 180 GLY A 189 1 10 HELIX 12 12 TYR A 190 GLN A 199 1 10 SITE 1 AC1 3 ASN A 103 GLY A 107 ASN A 137 CRYST1 26.961 66.902 94.959 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 0.037090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010531 0.00000