PDB Short entry for 1NCN HEADER IMMUNE SYSTEM 05-DEC-02 1NCN TITLE THE RECEPTOR-BINDING DOMAIN OF HUMAN B7-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: T LYMPHOCYTE ACTIVATION ANTIGEN CD86; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: IG V-TYPE DOMAIN; COMPND 5 SYNONYM: B7-2, ACTIVATION B7-2 ANTIGEN, CTLA-4 COUNTER- COMPND 6 RECEPTOR B7.2, B70, FUN-1, BU63; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: B7-2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3), B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS IG V, BETA STRANDS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,J.D.SCHWARTZ,S.C.ALMO,S.G.NATHENSON REVDAT 2 24-FEB-09 1NCN 1 VERSN REVDAT 1 11-MAR-03 1NCN 0 JRNL AUTH X.ZHANG,J.D.SCHWARTZ,S.C.ALMO,S.G.NATHENSON JRNL TITL CRYSTAL STRUCTURE OF THE RECEPTOR-BINDING DOMAIN JRNL TITL 2 OF HUMAN B7-2: INSIGHTS INTO ORGANIZATION AND JRNL TITL 3 SIGNALING JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 2586 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12606712 JRNL DOI 10.1073/PNAS.252771499 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH X.ZHANG,J.-C.D.SCHWARTZ,S.C.ALMO,S.G.NATHENSON REMARK 1 TITL EXPRESSION, REFOLDING, PURIFICATION, MOLECULAR REMARK 1 TITL 2 CHARACTERIZATION, CRYSTALLIZATION, AND PRELIMINARY REMARK 1 TITL 3 X-RAY ANALYSIS OF THE RECEPTOR BINDING DOMAIN OF REMARK 1 TITL 4 HUMAN B7-2 REMARK 1 REF PROTEIN EXPR.PURIF. V. 25 105 2002 REMARK 1 REFN ISSN 1046-5928 REMARK 1 DOI 10.1006/PREP.2002.1616 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 5842 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 629 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 491 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 53 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1804 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.98000 REMARK 3 B22 (A**2) : -3.55000 REMARK 3 B33 (A**2) : -6.43000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.40 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) : 1.530 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.550 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.550 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.670 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 18.26 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NCN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-DEC-02. REMARK 100 THE RCSB ID CODE IS RCSB017766. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-99 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 : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96110, 0.98000, 0.98019 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, NAAC, TRIS-HCL, PH 8.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 28.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.50500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.34500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.50500 REMARK 290 SMTRY3 4 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 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 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 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 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 GLU A 9 -152.84 -107.59 REMARK 500 SER A 62 119.88 -162.35 REMARK 500 THR A 93 -87.84 -59.95 REMARK 500 GLU B 9 -145.92 -119.28 REMARK 500 PRO B 92 -36.83 -35.69 REMARK 500 HIS B 99 144.30 -176.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I85 RELATED DB: PDB REMARK 900 THE COMPLEX BETWEEN THE RECEPTOR-BINDING DOMAIN OF HUMAN REMARK 900 B7-2 AND DIMERIC CTLA-4 DBREF 1NCN A 1 109 UNP P42081 CD86_HUMAN 26 134 DBREF 1NCN B 1 109 UNP P42081 CD86_HUMAN 26 134 SEQADV 1NCN MET A 0 UNP P42081 INITIATING METHIONINE SEQADV 1NCN MET B 0 UNP P42081 INITIATING METHIONINE SEQRES 1 A 110 MET LEU LYS ILE GLN ALA TYR PHE ASN GLU THR ALA ASP SEQRES 2 A 110 LEU PRO CYS GLN PHE ALA ASN SER GLN ASN GLN SER LEU SEQRES 3 A 110 SER GLU LEU VAL VAL PHE TRP GLN ASP GLN GLU ASN LEU SEQRES 4 A 110 VAL LEU ASN GLU VAL TYR LEU GLY LYS GLU LYS PHE ASP SEQRES 5 A 110 SER VAL HIS SER LYS TYR MET GLY ARG THR SER PHE ASP SEQRES 6 A 110 SER ASP SER TRP THR LEU ARG LEU HIS ASN LEU GLN ILE SEQRES 7 A 110 LYS ASP LYS GLY LEU TYR GLN CYS ILE ILE HIS HIS LYS SEQRES 8 A 110 LYS PRO THR GLY MET ILE ARG ILE HIS GLN MET ASN SER SEQRES 9 A 110 GLU LEU SER VAL LEU ALA SEQRES 1 B 110 MET LEU LYS ILE GLN ALA TYR PHE ASN GLU THR ALA ASP SEQRES 2 B 110 LEU PRO CYS GLN PHE ALA ASN SER GLN ASN GLN SER LEU SEQRES 3 B 110 SER GLU LEU VAL VAL PHE TRP GLN ASP GLN GLU ASN LEU SEQRES 4 B 110 VAL LEU ASN GLU VAL TYR LEU GLY LYS GLU LYS PHE ASP SEQRES 5 B 110 SER VAL HIS SER LYS TYR MET GLY ARG THR SER PHE ASP SEQRES 6 B 110 SER ASP SER TRP THR LEU ARG LEU HIS ASN LEU GLN ILE SEQRES 7 B 110 LYS ASP LYS GLY LEU TYR GLN CYS ILE ILE HIS HIS LYS SEQRES 8 B 110 LYS PRO THR GLY MET ILE ARG ILE HIS GLN MET ASN SER SEQRES 9 B 110 GLU LEU SER VAL LEU ALA HELIX 1 1 SER A 24 SER A 26 5 3 HELIX 2 2 GLN A 76 LYS A 80 5 5 HELIX 3 3 SER B 24 SER B 26 5 3 HELIX 4 4 GLN B 76 LYS B 80 5 5 SHEET 1 A 6 LEU A 1 TYR A 6 0 SHEET 2 A 6 MET A 95 LEU A 108 1 O GLU A 104 N ILE A 3 SHEET 3 A 6 GLY A 81 LYS A 90 -1 N HIS A 89 O ILE A 96 SHEET 4 A 6 LEU A 28 ASP A 34 -1 N PHE A 31 O ILE A 86 SHEET 5 A 6 VAL A 39 TYR A 44 -1 O LEU A 40 N TRP A 32 SHEET 6 A 6 LYS A 47 GLU A 48 -1 O LYS A 47 N TYR A 44 SHEET 1 B 3 ALA A 11 PRO A 14 0 SHEET 2 B 3 THR A 69 LEU A 72 -1 O LEU A 70 N LEU A 13 SHEET 3 B 3 THR A 61 ASP A 64 -1 N ASP A 64 O THR A 69 SHEET 1 C 6 LEU B 1 TYR B 6 0 SHEET 2 C 6 GLY B 94 LEU B 108 1 O GLU B 104 N LEU B 1 SHEET 3 C 6 GLY B 81 LYS B 91 -1 N CYS B 85 O MET B 101 SHEET 4 C 6 LEU B 28 ASP B 34 -1 N PHE B 31 O ILE B 86 SHEET 5 C 6 VAL B 39 TYR B 44 -1 O LEU B 40 N TRP B 32 SHEET 6 C 6 LYS B 47 LYS B 49 -1 O LYS B 49 N GLU B 42 SHEET 1 D 3 ALA B 11 PRO B 14 0 SHEET 2 D 3 THR B 69 LEU B 72 -1 O LEU B 70 N LEU B 13 SHEET 3 D 3 THR B 61 ASP B 64 -1 N SER B 62 O ARG B 71 SSBOND 1 CYS A 15 CYS A 85 1555 1555 2.02 SSBOND 2 CYS B 15 CYS B 85 1555 1555 2.04 CRYST1 56.690 63.010 58.610 90.00 90.00 90.00 P 21 21 2 8 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 0.017640 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017062 0.00000