HEADER IMMUNE SYSTEM 23-OCT-06 2NMS TITLE THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE INHIBITOR TITLE 2 RECEPTOR EXPRESSED ON MYELOID CELLS IREM-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMRF35-LIKE-MOLECULE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN, RESIDUES 21-140; COMPND 5 SYNONYM: CLM-1, IMMUNE RECEPTOR EXPRESSED ON MYELOID CELLS PROTEIN 1, COMPND 6 IREM-1, IMMUNOGLOBULIN SUPERFAMILY MEMBER 13, NK INHIBITORY RECEPTOR, COMPND 7 CD300 ANTIGEN LIKE FAMILY MEMBER F, IGSF13, IREM-1 MYELOID RECEPTOR COMPND 8 EXTRACELLULAR DOMAIN 1; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: MYELOID CELLS; SOURCE 6 GENE: CD300LF, CLM1, IGSF13, IREM1, NKIR; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS IG-SUPERFAMILY, IG-V, NKP44-LIKE, MYELOID IG-LIKE RECEPTOR, KEYWDS 2 INHIBITORY RECEPTOR, MYELO-MONOCYTIC CELLS, NEGATIVE REGULATION OF KEYWDS 3 LEUKOCYTE, MEMBRANE PROTEIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR N.DIMASI,J.A.MARQUEZ REVDAT 6 25-OCT-23 2NMS 1 SEQADV REVDAT 5 24-FEB-09 2NMS 1 VERSN REVDAT 4 13-MAR-07 2NMS 1 JRNL REVDAT 3 02-JAN-07 2NMS 1 JRNL REVDAT 2 14-NOV-06 2NMS 1 JRNL REVDAT 1 07-NOV-06 2NMS 0 JRNL AUTH J.A.MARQUEZ,E.GALFRE,F.DUPEUX,D.FLOT,O.MORAN,N.DIMASI JRNL TITL THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE JRNL TITL 2 INHIBITOR RECEPTOR EXPRESSED ON MYELOID CELLS IREM-1. JRNL REF J.MOL.BIOL. V. 367 310 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17275839 JRNL DOI 10.1016/J.JMB.2007.01.011 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.67 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) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 3936 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) : 0.218 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 201 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE : 0.4290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.076 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.47000 REMARK 3 B22 (A**2) : 3.47000 REMARK 3 B33 (A**2) : -6.93000 REMARK 3 B12 (A**2) : 5.66000 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) : 0.30 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) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.240 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.610 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.820 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.540 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.870 ; 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 2NMS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000040053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : PT COATED MIRRORS, MICROFOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 225 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3936 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 4.930 REMARK 200 R MERGE (I) : 0.09670 REMARK 200 R SYM (I) : 0.14200 REMARK 200 FOR THE DATA SET : 0.0967 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.01 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : 0.45500 REMARK 200 FOR SHELL : 4.170 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1ZOX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25M POTASSIUM THIOCYANATE, 25% (W/V) REMARK 280 PEG MME 2000, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.00333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.00667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 48.00667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.00333 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 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 ARG A 17 REMARK 465 VAL A 130 REMARK 465 THR A 131 REMARK 465 GLN A 132 REMARK 465 GLU A 133 REMARK 465 GLU A 134 REMARK 465 THR A 135 REMARK 465 SER A 136 REMARK 465 SER A 137 REMARK 465 SER A 138 REMARK 465 PRO A 139 REMARK 465 THR A 140 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 87 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 129 C - N - CA ANGL. DEV. = 16.6 DEGREES REMARK 500 PRO A 129 C - N - CD ANGL. DEV. = -16.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 19 -33.17 -143.08 REMARK 500 ARG A 33 -1.18 77.06 REMARK 500 ASP A 61 40.76 -91.12 REMARK 500 SER A 71 -166.66 -102.86 REMARK 500 ASP A 78 -117.14 65.37 REMARK 500 ASP A 97 58.37 33.37 REMARK 500 ASP A 104 -173.74 -176.81 REMARK 500 LYS A 112 138.11 -179.82 REMARK 500 THR A 113 59.86 27.36 REMARK 500 ALA A 128 -107.27 -103.99 REMARK 500 REMARK 500 REMARK: NULL DBREF 2NMS A 21 140 UNP Q8TDQ1 CLM1_HUMAN 21 140 SEQADV 2NMS ARG A 17 UNP Q8TDQ1 CLONING ARTIFACT SEQADV 2NMS GLY A 18 UNP Q8TDQ1 CLONING ARTIFACT SEQADV 2NMS ILE A 19 UNP Q8TDQ1 CLONING ARTIFACT SEQADV 2NMS PRO A 20 UNP Q8TDQ1 CLONING ARTIFACT SEQRES 1 A 124 ARG GLY ILE PRO GLN ILE THR GLY PRO THR THR VAL ASN SEQRES 2 A 124 GLY LEU GLU ARG GLY SER LEU THR VAL GLN CYS VAL TYR SEQRES 3 A 124 ARG SER GLY TRP GLU THR TYR LEU LYS TRP TRP CYS ARG SEQRES 4 A 124 GLY ALA ILE TRP ARG ASP CYS LYS ILE LEU VAL LYS THR SEQRES 5 A 124 SER GLY SER GLU GLN GLU VAL LYS ARG ASP ARG VAL SER SEQRES 6 A 124 ILE LYS ASP ASN GLN LYS ASN ARG THR PHE THR VAL THR SEQRES 7 A 124 MET GLU ASP LEU MET LYS THR ASP ALA ASP THR TYR TRP SEQRES 8 A 124 CYS GLY ILE GLU LYS THR GLY ASN ASP LEU GLY VAL THR SEQRES 9 A 124 VAL GLN VAL THR ILE ASP PRO ALA PRO VAL THR GLN GLU SEQRES 10 A 124 GLU THR SER SER SER PRO THR FORMUL 2 HOH *50(H2 O) HELIX 1 1 MET A 99 ALA A 103 5 5 SHEET 1 A 5 ILE A 22 THR A 23 0 SHEET 2 A 5 LEU A 36 TYR A 42 -1 O VAL A 41 N THR A 23 SHEET 3 A 5 THR A 90 MET A 95 -1 O VAL A 93 N VAL A 38 SHEET 4 A 5 VAL A 80 ASN A 85 -1 N SER A 81 O THR A 94 SHEET 5 A 5 VAL A 75 ARG A 77 -1 N ARG A 77 O VAL A 80 SHEET 1 B 5 THR A 27 LEU A 31 0 SHEET 2 B 5 ASN A 115 ASP A 126 1 O THR A 124 N VAL A 28 SHEET 3 B 5 ASP A 104 LYS A 112 -1 N TYR A 106 O VAL A 121 SHEET 4 B 5 LEU A 50 ARG A 55 -1 N TRP A 52 O GLY A 109 SHEET 5 B 5 LYS A 63 LYS A 67 -1 O LEU A 65 N TRP A 53 SSBOND 1 CYS A 40 CYS A 108 1555 1555 2.02 SSBOND 2 CYS A 54 CYS A 62 1555 1555 2.02 CISPEP 1 ALA A 128 PRO A 129 0 -0.43 CRYST1 54.230 54.230 72.010 90.00 90.00 120.00 P 31 2 1 6 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 0.018440 0.010646 0.000000 0.00000 SCALE2 0.000000 0.021293 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013887 0.00000