HEADER DE NOVO PROTEIN 06-APR-11 3RFN TITLE EPITOPE BACKBONE GRAFTING BY COMPUTATIONAL DESIGN FOR IMPROVED TITLE 2 PRESENTATION OF LINEAR EPITOPES ON SCAFFOLD PROTEINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BB_1WNU_001; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 GENE: ALAXS, PH0574; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN GRAFTING, FLEXIBLE BACKBONE DESIGN, EPITOPE-SCAFFOLD, HIV, KEYWDS 2 IMMUNOGEN DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.L.AZOITEI,Y.A.BAN,J.P.JULIEN,S.BRYSON,A.SCHROETER,O.KALYUZHNIY, AUTHOR 2 J.R.PORTER,Y.ADACHI,D.BAKER,E.SZABO,E.F.PAI,W.R.SCHIEF REVDAT 4 26-JUL-17 3RFN 1 SOURCE REMARK REVDAT 3 18-JAN-12 3RFN 1 JRNL REVDAT 2 23-NOV-11 3RFN 1 JRNL REVDAT 1 09-NOV-11 3RFN 0 JRNL AUTH M.L.AZOITEI,Y.E.BAN,J.P.JULIEN,S.BRYSON,A.SCHROETER, JRNL AUTH 2 O.KALYUZHNIY,J.R.PORTER,Y.ADACHI,D.BAKER,E.F.PAI,W.R.SCHIEF JRNL TITL COMPUTATIONAL DESIGN OF HIGH-AFFINITY EPITOPE SCAFFOLDS BY JRNL TITL 2 BACKBONE GRAFTING OF A LINEAR EPITOPE. JRNL REF J.MOL.BIOL. V. 415 175 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22061265 JRNL DOI 10.1016/J.JMB.2011.10.003 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 13181 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 691 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1201 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 93.2 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15316 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 17.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 1.750 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02200 REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.44 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.13200 REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1WNU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M NACL, 0.1 M TRIS, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 46.90000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.90000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.05000 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 LEU A 153 REMARK 465 GLU A 154 REMARK 465 HIS A 155 REMARK 465 HIS A 156 REMARK 465 HIS A 157 REMARK 465 HIS A 158 REMARK 465 HIS A 159 REMARK 465 HIS A 160 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 ALA A 27 35.56 -148.98 REMARK 500 LEU A 93 49.69 -81.80 REMARK 500 PRO A 97 131.74 -28.36 REMARK 500 GLU A 109 123.95 -36.07 REMARK 500 TRP A 111 -53.57 -148.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 13 NE2 REMARK 620 2 HIS A 9 NE2 112.6 REMARK 620 3 HIS A 120 NE2 98.1 90.4 REMARK 620 4 CYS A 116 SG 141.2 91.0 112.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN CONSTRUCT CONSISTS OF UNP RESIDUES 2-154 WITH A C-TERMINAL REMARK 999 EXPRESSION TAG AND UNP RESIDUES 46-60 (FDRKPSDEEIREIER) REPLACED BY REMARK 999 EPITOPE AALELDKWAWAAMEA DBREF 3RFN A 2 45 UNP O58307 ALAXS_PYRHO 2 45 DBREF 3RFN A 61 154 UNP O58307 ALAXS_PYRHO 61 154 SEQADV 3RFN ALA A 22 UNP O58307 VAL 22 ENGINEERED MUTATION SEQADV 3RFN ALA A 23 UNP O58307 LEU 23 ENGINEERED MUTATION SEQADV 3RFN ALA A 26 UNP O58307 GLU 26 ENGINEERED MUTATION SEQADV 3RFN THR A 31 UNP O58307 TYR 31 ENGINEERED MUTATION SEQADV 3RFN HIS A 155 UNP O58307 EXPRESSION TAG SEQADV 3RFN HIS A 156 UNP O58307 EXPRESSION TAG SEQADV 3RFN HIS A 157 UNP O58307 EXPRESSION TAG SEQADV 3RFN HIS A 158 UNP O58307 EXPRESSION TAG SEQADV 3RFN HIS A 159 UNP O58307 EXPRESSION TAG SEQADV 3RFN HIS A 160 UNP O58307 EXPRESSION TAG SEQRES 1 A 159 TYR SER ILE GLU VAL ARG THR HIS SER ALA LEU HIS VAL SEQRES 2 A 159 VAL LYS GLY ALA VAL VAL LYS ALA ALA GLY SER ALA ALA SEQRES 3 A 159 LYS TRP THR THR SER THR TYR VAL LYS GLY ASN LYS GLY SEQRES 4 A 159 VAL LEU ILE VAL LYS ALA ALA LEU GLU LEU ASP LYS TRP SEQRES 5 A 159 ALA TRP ALA ALA MET GLU ALA LEU ALA ASN GLU LYS VAL SEQRES 6 A 159 LYS GLU ASN ALA PRO ILE LYS ILE TYR GLU LEU PRO ARG SEQRES 7 A 159 GLU GLU ALA GLU LYS MET PHE GLY GLU ASP MET TYR ASP SEQRES 8 A 159 LEU PHE PRO VAL PRO GLU ASP VAL ARG ILE LEU LYS VAL SEQRES 9 A 159 VAL VAL ILE GLU ASP TRP ASN VAL ASN ALA CYS ASN LYS SEQRES 10 A 159 GLU HIS THR LYS THR THR GLY GLU ILE GLY PRO ILE LYS SEQRES 11 A 159 ILE ARG LYS VAL ARG PHE ARG LYS SER LYS GLY LEU LEU SEQRES 12 A 159 GLU ILE HIS PHE GLU LEU LEU GLU LEU GLU HIS HIS HIS SEQRES 13 A 159 HIS HIS HIS HET ZN A 1 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *88(H2 O) HELIX 1 1 SER A 3 GLY A 24 1 22 HELIX 2 2 SER A 25 LYS A 28 5 4 HELIX 3 3 TRP A 53 ASN A 69 1 17 HELIX 4 4 ARG A 79 GLY A 87 1 9 HELIX 5 5 GLU A 88 TYR A 91 5 4 HELIX 6 6 THR A 123 GLY A 128 5 6 SHEET 1 A 4 TRP A 29 LYS A 36 0 SHEET 2 A 4 LYS A 39 LYS A 45 -1 O LYS A 39 N LYS A 36 SHEET 3 A 4 LEU A 143 GLU A 149 -1 O ILE A 146 N LEU A 42 SHEET 4 A 4 LYS A 131 ARG A 138 -1 N LYS A 134 O HIS A 147 SHEET 1 B 3 LYS A 73 PRO A 78 0 SHEET 2 B 3 ILE A 102 ILE A 108 -1 O VAL A 105 N TYR A 75 SHEET 3 B 3 ASN A 112 ALA A 115 -1 O ASN A 114 N VAL A 106 LINK NE2 HIS A 13 ZN ZN A 1 1555 1555 2.10 LINK NE2 HIS A 9 ZN ZN A 1 1555 1555 2.18 LINK NE2 HIS A 120 ZN ZN A 1 1555 1555 2.20 LINK SG CYS A 116 ZN ZN A 1 1555 1555 2.44 SITE 1 AC1 4 HIS A 9 HIS A 13 CYS A 116 HIS A 120 CRYST1 93.800 36.100 46.300 90.00 99.40 90.00 C 1 2 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 0.010661 0.000000 0.001759 0.00000 SCALE2 0.000000 0.027739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021938 0.00000 MASTER 270 0 1 6 7 0 1 6 0 0 0 13 END