HEADER DE NOVO PROTEIN 07-MAR-14 4PSJ TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM (NESG) TARGET OR464. COMPND MOL_ID: 1; COMPND 2 MOLECULE: OR464; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: ARTIFICIAL GENE; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15_NESG; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: OR464-15.1 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 ENGINEERED PROTEIN, NESG, OR464, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,F.PARMEGGIANI,J.SEETHARAMAN,P.-S.HUANG,H.JANJUA,R.XIAO, AUTHOR 2 M.MAGLAQUI,K.PARK,J.K.EVERETT,T.B.ACTON,D.BAKER,G.T.MONTELIONE, AUTHOR 3 L.TONG,J.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 20-SEP-23 4PSJ 1 REMARK REVDAT 1 26-MAR-14 4PSJ 0 JRNL AUTH S.VOROBIEV,F.PARMEGGIANI,J.SEETHARAMAN,P.-S.HUANG,H.JANJUA, JRNL AUTH 2 R.XIAO,M.MAGLAQUI,K.PARK,J.K.EVERETT,T.B.ACTON,D.BAKER, JRNL AUTH 3 G.T.MONTELIONE,L.TONG,J.HUNT JRNL TITL CRYSTAL STRUCTURE OF ENGINEERED PROTEIN OR464. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 27919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1403 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 31.9150 - 4.2890 0.97 2755 138 0.1740 0.2420 REMARK 3 2 4.2890 - 3.4060 0.98 2831 140 0.1550 0.2010 REMARK 3 3 3.4060 - 2.9760 1.00 2833 151 0.1790 0.2230 REMARK 3 4 2.9760 - 2.7040 1.00 2844 142 0.1830 0.2240 REMARK 3 5 2.7040 - 2.5100 1.00 2874 149 0.1940 0.2790 REMARK 3 6 2.5100 - 2.3620 1.00 2843 156 0.1940 0.2830 REMARK 3 7 2.3620 - 2.2440 0.99 2780 142 0.2080 0.2580 REMARK 3 8 2.2440 - 2.1460 0.94 2666 167 0.1950 0.3030 REMARK 3 9 2.1460 - 2.0640 0.79 2295 102 0.2040 0.2860 REMARK 3 10 2.0640 - 1.9920 0.65 1795 116 0.2090 0.2680 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 : 0.86 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 32.17 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.530 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.01600 REMARK 3 B22 (A**2) : -6.72400 REMARK 3 B33 (A**2) : 8.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -5.34200 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 2012 REMARK 3 ANGLE : 1.054 2747 REMARK 3 CHIRALITY : 0.067 346 REMARK 3 PLANARITY : 0.004 360 REMARK 3 DIHEDRAL : 17.075 755 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 7.3419 0.5710 7.0469 REMARK 3 T TENSOR REMARK 3 T11: 0.1085 T22: 0.1253 REMARK 3 T33: 0.1746 T12: -0.0267 REMARK 3 T13: -0.0279 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.4273 L22: 2.3103 REMARK 3 L33: 1.9631 L12: -0.5281 REMARK 3 L13: -0.3768 L23: 0.4658 REMARK 3 S TENSOR REMARK 3 S11: 0.0330 S12: -0.0870 S13: -0.0082 REMARK 3 S21: 0.1957 S22: 0.0115 S23: 0.0260 REMARK 3 S31: -0.0014 S32: -0.0058 S33: -0.0489 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 4PSJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 0.97942 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 : 28015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 93.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.6000 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 (%) : 68.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 3RFJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5). RESERVOIR SOLUTION: 25% PEG REMARK 280 3350, 0.1M BIS-TRIS, MICROBATCH CRYSTALLIZATION UNDER OIL, REMARK 280 TEMPERATURE 291K, PH 5.5 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 25.72750 REMARK 290 SMTRY3 2 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 GLY A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 GLY A 264 REMARK 465 SER A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 465 HIS A 271 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 LEU A 69 77.15 -118.73 REMARK 500 ASN A 80 -153.42 -99.74 REMARK 500 ASN A 102 -151.44 -108.75 REMARK 500 ASN A 126 -152.85 -101.63 REMARK 500 ASN A 150 -145.53 -108.34 REMARK 500 LEU A 163 52.96 -90.59 REMARK 500 ASN A 174 -155.95 -118.30 REMARK 500 ASN A 198 -161.72 -120.17 REMARK 500 LEU A 211 57.02 -90.64 REMARK 500 ASN A 222 -146.99 -116.12 REMARK 500 ASN A 246 -167.52 -110.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR464 RELATED DB: TARGETTRACK DBREF 4PSJ A 1 271 PDB 4PSJ 4PSJ 1 271 SEQRES 1 A 271 MET GLY HIS HIS HIS HIS HIS HIS THR ILE THR VAL SER SEQRES 2 A 271 THR PRO ILE LYS GLN ILE PHE PRO ASP ASP ALA PHE ALA SEQRES 3 A 271 GLU THR ILE LYS ALA ASN LEU LYS LYS LYS SER VAL THR SEQRES 4 A 271 ASP ALA VAL THR GLN ASN GLU LEU ASN SER ILE ASP GLN SEQRES 5 A 271 ILE ASN ALA ASN ASN SER ASP ILE LYS SER VAL GLN GLY SEQRES 6 A 271 ILE GLN TYR LEU PRO ASN VAL ARG GLN LEU ASN LEU GLY SEQRES 7 A 271 GLY ASN LYS LEU HIS ASP ILE SER ALA LEU LYS GLU LEU SEQRES 8 A 271 THR ASN LEU GLY TRP LEU ASN LEU SER SER ASN LYS ILE SEQRES 9 A 271 GLU LYS LEU PRO GLN GLY LEU PHE GLU SER LEU THR THR SEQRES 10 A 271 LEU THR GLN LEU ASN LEU SER ASN ASN GLN ILE THR SER SEQRES 11 A 271 LEU PRO GLN GLY LEU PHE GLU SER LEU ALA SER LEU THR SEQRES 12 A 271 GLN LEU ASN LEU SER ASN ASN GLN ILE THR SER LEU PRO SEQRES 13 A 271 GLN GLY LEU PHE GLU SER LEU THR ASN LEU THR GLN LEU SEQRES 14 A 271 ASN LEU SER ASN ASN GLN ILE THR SER LEU PRO GLN GLY SEQRES 15 A 271 LEU PHE GLU SER LEU THR ASN LEU THR GLN LEU ASN LEU SEQRES 16 A 271 SER ASN ASN GLN ILE THR SER LEU PRO GLN GLY LEU PHE SEQRES 17 A 271 GLU SER LEU THR SER LEU THR GLN LEU ASN LEU SER ASN SEQRES 18 A 271 ASN GLN ILE THR SER LEU PRO GLN GLY LEU PHE GLU SER SEQRES 19 A 271 LEU THR ASN LEU LYS GLN LEU ASN LEU SER GLY ASN GLN SEQRES 20 A 271 ILE GLN SER LEU PRO GLN GLY LEU HIS GLU SER LEU THR SEQRES 21 A 271 GLN LEU THR GLY SER HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *169(H2 O) HELIX 1 1 ILE A 16 PHE A 20 1 5 HELIX 2 2 ASP A 22 LEU A 33 1 12 HELIX 3 3 THR A 43 SER A 49 1 7 HELIX 4 4 GLY A 65 LEU A 69 5 5 HELIX 5 5 ILE A 85 LYS A 89 5 5 HELIX 6 6 GLY A 254 THR A 263 1 10 SHEET 1 A 2 THR A 14 PRO A 15 0 SHEET 2 A 2 ALA A 41 VAL A 42 -1 O VAL A 42 N THR A 14 SHEET 1 B 9 GLN A 52 ASN A 54 0 SHEET 2 B 9 GLN A 74 ASN A 76 1 O ASN A 76 N ILE A 53 SHEET 3 B 9 TRP A 96 ASN A 98 1 O ASN A 98 N LEU A 75 SHEET 4 B 9 GLN A 120 ASN A 122 1 O GLN A 120 N LEU A 97 SHEET 5 B 9 GLN A 144 ASN A 146 1 O ASN A 146 N LEU A 121 SHEET 6 B 9 GLN A 168 ASN A 170 1 O ASN A 170 N LEU A 145 SHEET 7 B 9 GLN A 192 ASN A 194 1 O ASN A 194 N LEU A 169 SHEET 8 B 9 GLN A 216 ASN A 218 1 O ASN A 218 N LEU A 193 SHEET 9 B 9 GLN A 240 ASN A 242 1 O ASN A 242 N LEU A 217 CRYST1 31.916 51.455 69.005 90.00 90.98 90.00 P 1 21 1 2 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 0.031332 0.000000 0.000538 0.00000 SCALE2 0.000000 0.019434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014494 0.00000