HEADER DE NOVO PROTEIN 25-OCT-12 4HQD TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET OR265. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED PROTEIN OR265; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 GENE: ENGINEERED PROTEIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21_NESG, OR265-21.1 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, ENGINEERED PROTEIN, NORTHEAST KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, NESG, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,M.SU,F.PARMEGGIANI,J.SEETHARAMAN,P.-S.HUANG,M.MAGLAQUI, AUTHOR 2 R.XIAO,D.LEE,J.K.EVERETT,T.B.ACTON,D.BAKER,G.T.MONTELIONE,L.TONG, AUTHOR 3 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 20-SEP-23 4HQD 1 REMARK REVDAT 2 24-JAN-18 4HQD 1 AUTHOR JRNL REVDAT 1 14-NOV-12 4HQD 0 JRNL AUTH S.VOROBIEV,M.SU,F.PARMEGGIANI,J.SEETHARAMAN,P.-S.HUANG, JRNL AUTH 2 M.MAGLAQUI,R.XIAO,D.LEE,J.K.EVERETT,T.B.ACTON,D.BAKER, JRNL AUTH 3 G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF ENGINEERED PROTEIN OR265. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 20800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 990 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 34.9960 - 4.6520 0.99 2890 131 0.1790 0.1900 REMARK 3 2 4.6520 - 3.6930 0.98 2828 149 0.1810 0.1880 REMARK 3 3 3.6930 - 3.2270 0.98 2879 133 0.1900 0.2030 REMARK 3 4 3.2270 - 2.9320 0.98 2849 142 0.2070 0.3020 REMARK 3 5 2.9320 - 2.7220 0.99 2839 137 0.2140 0.2780 REMARK 3 6 2.7220 - 2.5620 0.99 2867 166 0.2260 0.2940 REMARK 3 7 2.5620 - 2.4330 0.91 2658 132 0.2590 0.2900 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 43.35 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.720 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.83000 REMARK 3 B22 (A**2) : -1.56000 REMARK 3 B33 (A**2) : 8.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -7.36600 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 : 0.006 2471 REMARK 3 ANGLE : 1.169 3316 REMARK 3 CHIRALITY : 0.087 368 REMARK 3 PLANARITY : 0.005 438 REMARK 3 DIHEDRAL : 14.339 946 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 25.2178 0.5106 6.2982 REMARK 3 T TENSOR REMARK 3 T11: 0.0490 T22: -0.0113 REMARK 3 T33: -0.0152 T12: -0.0280 REMARK 3 T13: -0.1207 T23: -0.0618 REMARK 3 L TENSOR REMARK 3 L11: 0.0018 L22: 0.0009 REMARK 3 L33: 0.0029 L12: 0.0003 REMARK 3 L13: -0.0011 L23: -0.0020 REMARK 3 S TENSOR REMARK 3 S11: 0.0449 S12: 0.0025 S13: -0.0065 REMARK 3 S21: -0.0069 S22: -0.0454 S23: 0.0199 REMARK 3 S31: -0.0141 S32: 0.0130 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 8.2902 -6.7216 -27.1113 REMARK 3 T TENSOR REMARK 3 T11: 0.0397 T22: 0.0798 REMARK 3 T33: 0.0771 T12: 0.0042 REMARK 3 T13: 0.0165 T23: 0.0190 REMARK 3 L TENSOR REMARK 3 L11: 0.0027 L22: -0.0004 REMARK 3 L33: 0.0051 L12: 0.0001 REMARK 3 L13: -0.0000 L23: -0.0008 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: -0.0046 S13: -0.0021 REMARK 3 S21: -0.0010 S22: -0.0039 S23: 0.0068 REMARK 3 S31: -0.0037 S32: -0.0033 S33: 0.0000 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 4HQD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000075788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97905 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20809 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.21200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 4HB5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG 400, 0.1M LITHIUM SULFATE, REMARK 280 0.1M HEPES, PH 7.5, MICROBATCH CRYSTALLIZATION UNDER OIL, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.23050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: MONOMER,17.1 KD,98.1% 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 GLU A 145 REMARK 465 HIS A 146 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 MET B 1 REMARK 465 LEU B 162 REMARK 465 GLU B 163 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 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 29 99.69 -63.48 REMARK 500 ASP A 133 -160.69 -78.34 REMARK 500 GLN A 158 -164.76 -101.02 REMARK 500 TRP A 161 -41.03 -143.89 REMARK 500 GLU B 3 152.82 179.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HB5 RELATED DB: PDB REMARK 900 RELATED ID: 4GPM RELATED DB: PDB REMARK 900 RELATED ID: 4GMR RELATED DB: PDB REMARK 900 RELATED ID: NESG-OR265 RELATED DB: TARGETTRACK DBREF 4HQD A 1 169 PDB 4HQD 4HQD 1 169 DBREF 4HQD B 1 169 PDB 4HQD 4HQD 1 169 SEQRES 1 A 169 MET SER GLU LEU GLY LYS ARG LEU ILE GLU ALA ALA GLU SEQRES 2 A 169 ASN GLY ASN LYS ASP ARG VAL LYS ASP LEU ILE GLU ASN SEQRES 3 A 169 GLY ALA ASP VAL ASN ALA SER ASP SER ASP GLY ARG THR SEQRES 4 A 169 PRO LEU HIS TYR ALA ALA LYS GLU GLY HIS LYS GLU ILE SEQRES 5 A 169 VAL LYS LEU LEU ILE SER LYS GLY ALA ASP VAL ASN ALA SEQRES 6 A 169 LYS ASP SER ASP GLY ARG THR PRO LEU HIS TYR ALA ALA SEQRES 7 A 169 LYS GLU GLY HIS LYS GLU ILE VAL LYS LEU LEU ILE SER SEQRES 8 A 169 LYS GLY ALA ASP VAL ASN ALA LYS ASP SER ASP GLY ARG SEQRES 9 A 169 THR PRO LEU HIS TYR ALA ALA LYS GLU GLY HIS LYS GLU SEQRES 10 A 169 ILE VAL LYS LEU LEU ILE SER LYS GLY ALA ASP VAL ASN SEQRES 11 A 169 THR SER ASP SER ASP GLY ARG THR PRO LEU ASP LEU ALA SEQRES 12 A 169 ARG GLU HIS GLY ASN GLU GLU ILE VAL LYS LEU LEU GLU SEQRES 13 A 169 LYS GLN GLY GLY TRP LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 169 MET SER GLU LEU GLY LYS ARG LEU ILE GLU ALA ALA GLU SEQRES 2 B 169 ASN GLY ASN LYS ASP ARG VAL LYS ASP LEU ILE GLU ASN SEQRES 3 B 169 GLY ALA ASP VAL ASN ALA SER ASP SER ASP GLY ARG THR SEQRES 4 B 169 PRO LEU HIS TYR ALA ALA LYS GLU GLY HIS LYS GLU ILE SEQRES 5 B 169 VAL LYS LEU LEU ILE SER LYS GLY ALA ASP VAL ASN ALA SEQRES 6 B 169 LYS ASP SER ASP GLY ARG THR PRO LEU HIS TYR ALA ALA SEQRES 7 B 169 LYS GLU GLY HIS LYS GLU ILE VAL LYS LEU LEU ILE SER SEQRES 8 B 169 LYS GLY ALA ASP VAL ASN ALA LYS ASP SER ASP GLY ARG SEQRES 9 B 169 THR PRO LEU HIS TYR ALA ALA LYS GLU GLY HIS LYS GLU SEQRES 10 B 169 ILE VAL LYS LEU LEU ILE SER LYS GLY ALA ASP VAL ASN SEQRES 11 B 169 THR SER ASP SER ASP GLY ARG THR PRO LEU ASP LEU ALA SEQRES 12 B 169 ARG GLU HIS GLY ASN GLU GLU ILE VAL LYS LEU LEU GLU SEQRES 13 B 169 LYS GLN GLY GLY TRP LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *81(H2 O) HELIX 1 1 GLU A 3 ASN A 14 1 12 HELIX 2 2 ASN A 16 ASN A 26 1 11 HELIX 3 3 THR A 39 GLY A 48 1 10 HELIX 4 4 HIS A 49 LYS A 59 1 11 HELIX 5 5 THR A 72 GLY A 81 1 10 HELIX 6 6 HIS A 82 LYS A 92 1 11 HELIX 7 7 THR A 105 GLY A 114 1 10 HELIX 8 8 HIS A 115 LYS A 125 1 11 HELIX 9 9 THR A 138 ALA A 143 1 6 HELIX 10 10 ASN A 148 LYS A 157 1 10 HELIX 11 11 GLU B 3 ASN B 14 1 12 HELIX 12 12 ASN B 16 ASN B 26 1 11 HELIX 13 13 THR B 39 GLY B 48 1 10 HELIX 14 14 HIS B 49 LYS B 59 1 11 HELIX 15 15 THR B 72 GLY B 81 1 10 HELIX 16 16 HIS B 82 LYS B 92 1 11 HELIX 17 17 THR B 105 GLY B 114 1 10 HELIX 18 18 HIS B 115 LYS B 125 1 11 HELIX 19 19 THR B 138 GLY B 147 1 10 HELIX 20 20 ASN B 148 LYS B 157 1 10 CRYST1 69.004 30.461 70.061 90.00 92.68 90.00 P 1 21 1 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 0.014492 0.000000 0.000678 0.00000 SCALE2 0.000000 0.032829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014289 0.00000