HEADER IMMUNE SYSTEM 07-OCT-15 5E56 TITLE CRYSTAL STRUCTURE OF MOUSE CTLA-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4,CTLA-4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: CTLA4, CD152; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNOGLOBULIN VARIABLE DOMAIN, IG-FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,D.SAMANTA,J.B.BONANNO,S.C.ALMO REVDAT 4 20-NOV-24 5E56 1 REMARK REVDAT 3 27-SEP-23 5E56 1 REMARK LINK REVDAT 2 02-MAR-16 5E56 1 AUTHOR JRNL REVDAT 1 28-OCT-15 5E56 0 JRNL AUTH A.A.FEDOROV,E.V.FEDOROV,D.SAMANTA,J.B.BONANNO,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF MOUSE CTLA-4 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17192 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.110 REMARK 3 FREE R VALUE TEST SET COUNT : 707 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 27.8101 - 2.5711 0.96 3290 138 0.1703 0.1759 REMARK 3 2 2.5711 - 2.0410 1.00 3315 135 0.1834 0.2046 REMARK 3 3 2.0410 - 1.7830 1.00 3319 135 0.1653 0.2235 REMARK 3 4 1.7830 - 1.6200 1.00 3316 144 0.2041 0.2349 REMARK 3 5 1.6200 - 1.5039 1.00 3245 155 0.2379 0.2866 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.670 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 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 : 0.006 976 REMARK 3 ANGLE : 1.064 1337 REMARK 3 CHIRALITY : 0.070 153 REMARK 3 PLANARITY : 0.005 178 REMARK 3 DIHEDRAL : 12.042 352 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): 17.8769 16.9858 13.2770 REMARK 3 T TENSOR REMARK 3 T11: 0.1763 T22: 0.1611 REMARK 3 T33: 0.1706 T12: -0.0236 REMARK 3 T13: 0.0096 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 2.7577 L22: 1.6178 REMARK 3 L33: 3.9549 L12: 0.0962 REMARK 3 L13: 0.0983 L23: 0.7786 REMARK 3 S TENSOR REMARK 3 S11: 0.0021 S12: -0.2842 S13: 0.0806 REMARK 3 S21: 0.1734 S22: -0.0432 S23: 0.0023 REMARK 3 S31: -0.2821 S32: 0.0280 S33: 0.0420 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 5E56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.504 REMARK 200 RESOLUTION RANGE LOW (A) : 27.805 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: 1DQT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NA/K PHOSPHATE, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.0K 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 23.76900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.29900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.76900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.29900 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 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 PRO A 117 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 THR A 40 -119.99 -114.30 REMARK 500 ASP A 42 -131.32 -132.58 REMARK 500 GLU A 72 -106.59 60.26 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 NA A 201 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 60 O REMARK 620 2 TYR A 63 O 86.3 REMARK 620 3 CYS A 66 O 92.2 84.7 REMARK 620 4 HOH A 318 O 84.5 81.0 165.5 REMARK 620 5 HOH A 327 O 177.7 95.7 89.1 94.8 REMARK 620 6 HOH A 367 O 91.1 177.3 95.8 98.4 87.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DQT RELATED DB: PDB REMARK 900 THE ENTRY IS THE SAME PROTEIN CRYSTALLIZED AT DIFFERENT CONDITIONS, REMARK 900 DIFFERENT SPACE GROUP, AND LOWER RESOLUTION REMARK 900 RELATED ID: 5E5M RELATED DB: PDB DBREF 5E56 A 1 117 UNP P09793 CTLA4_MOUSE 38 154 SEQRES 1 A 117 ILE GLN VAL THR GLN PRO SER VAL VAL LEU ALA SER SER SEQRES 2 A 117 HIS GLY VAL ALA SER PHE PRO CYS GLU TYR SER PRO SER SEQRES 3 A 117 HIS ASN THR ASP GLU VAL ARG VAL THR VAL LEU ARG GLN SEQRES 4 A 117 THR ASN ASP GLN MET THR GLU VAL CYS ALA THR THR PHE SEQRES 5 A 117 THR GLU LYS ASN THR VAL GLY PHE LEU ASP TYR PRO PHE SEQRES 6 A 117 CYS SER GLY THR PHE ASN GLU SER ARG VAL ASN LEU THR SEQRES 7 A 117 ILE GLN GLY LEU ARG ALA VAL ASP THR GLY LEU TYR LEU SEQRES 8 A 117 CYS LYS VAL GLU LEU MET TYR PRO PRO PRO TYR PHE VAL SEQRES 9 A 117 GLY MET GLY ASN GLY THR GLN ILE TYR VAL ILE ASP PRO HET NA A 201 1 HETNAM NA SODIUM ION FORMUL 2 NA NA 1+ FORMUL 3 HOH *72(H2 O) HELIX 1 AA1 ARG A 83 THR A 87 5 5 SHEET 1 AA1 5 GLN A 2 THR A 4 0 SHEET 2 AA1 5 ALA A 17 SER A 24 -1 O SER A 24 N GLN A 2 SHEET 3 AA1 5 ARG A 74 ILE A 79 -1 O ILE A 79 N ALA A 17 SHEET 4 AA1 5 CYS A 66 ASN A 71 -1 N ASN A 71 O ARG A 74 SHEET 5 AA1 5 VAL A 58 GLY A 59 -1 N GLY A 59 O GLY A 68 SHEET 1 AA2 5 VAL A 8 LEU A 10 0 SHEET 2 AA2 5 THR A 110 TYR A 113 1 O GLN A 111 N VAL A 9 SHEET 3 AA2 5 GLY A 88 TYR A 98 -1 N GLY A 88 O ILE A 112 SHEET 4 AA2 5 GLU A 31 GLN A 39 -1 N GLN A 39 O LEU A 89 SHEET 5 AA2 5 MET A 44 PHE A 52 -1 O VAL A 47 N VAL A 36 SHEET 1 AA3 4 VAL A 8 LEU A 10 0 SHEET 2 AA3 4 THR A 110 TYR A 113 1 O GLN A 111 N VAL A 9 SHEET 3 AA3 4 GLY A 88 TYR A 98 -1 N GLY A 88 O ILE A 112 SHEET 4 AA3 4 PHE A 103 MET A 106 -1 O PHE A 103 N LEU A 96 SSBOND 1 CYS A 21 CYS A 92 1555 1555 2.03 SSBOND 2 CYS A 48 CYS A 66 1555 1555 2.05 LINK O PHE A 60 NA NA A 201 1555 1555 2.45 LINK O TYR A 63 NA NA A 201 1555 1555 2.25 LINK O CYS A 66 NA NA A 201 1555 1555 2.27 LINK NA NA A 201 O HOH A 318 1555 3545 2.25 LINK NA NA A 201 O HOH A 327 1555 3545 2.55 LINK NA NA A 201 O HOH A 367 1555 1555 2.37 CISPEP 1 SER A 24 PRO A 25 0 -6.93 CISPEP 2 TYR A 98 PRO A 99 0 -0.36 CISPEP 3 PRO A 100 PRO A 101 0 0.29 SITE 1 AC1 7 ASN A 41 PHE A 60 TYR A 63 CYS A 66 SITE 2 AC1 7 HOH A 318 HOH A 327 HOH A 367 CRYST1 47.538 36.598 65.149 90.00 105.13 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 0.021036 0.000000 0.005686 0.00000 SCALE2 0.000000 0.027324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015900 0.00000