HEADER EXTRACELLULAR MODULE 23-OCT-98 1BY2 TITLE STRUCTURE OF M2BP SCAVENGER RECEPTOR CYSTEINE-RICH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAC-2 BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SCAVENGER RECEPTOR CYSTEINE-RICH (SRCR) DOMAIN; COMPND 5 SYNONYM: TUMOR-ASSOCIATED ANTIGEN 90K; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: 293-EBNA; SOURCE 6 ORGAN: KIDNEY; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: 293-EBNA; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PCEP-PU KEYWDS EXTRACELLULAR MODULE, SCAVENGER RECEPTOR, TUMOUR-ASSOCIATED ANTIGEN, KEYWDS 2 EXTRACELLULAR MATRIX, GLYCOSYLATED PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.HOHENESTER,T.SASAKI,R.TIMPL REVDAT 4 29-JUL-20 1BY2 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 1BY2 1 VERSN REVDAT 2 24-FEB-09 1BY2 1 VERSN REVDAT 1 18-MAY-99 1BY2 0 JRNL AUTH E.HOHENESTER,T.SASAKI,R.TIMPL JRNL TITL CRYSTAL STRUCTURE OF A SCAVENGER RECEPTOR CYSTEINE-RICH JRNL TITL 2 DOMAIN SHEDS LIGHT ON AN ANCIENT SUPERFAMILY. JRNL REF NAT.STRUCT.BIOL. V. 6 228 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10074941 JRNL DOI 10.1038/6669 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.SASAKI,C.BRAKEBUSCH,J.ENGEL,R.TIMPL REMARK 1 TITL MAC-2 BINDING PROTEIN IS A CELL-ADHESIVE PROTEIN OF THE REMARK 1 TITL 2 EXTRACELLULAR MATRIX WHICH SELF-ASSEMBLES INTO RING-LIKE REMARK 1 TITL 3 STRUCTURES AND BINDS BETA1 INTEGRINS, COLLAGENS AND REMARK 1 TITL 4 FIBRONECTIN REMARK 1 REF EMBO J. V. 17 1606 1998 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.RESNICK,A.PEARSON,M.KRIEGER REMARK 1 TITL THE SRCR SUPERFAMILY: A FAMILY REMINISCENT OF THE IG REMARK 1 TITL 2 SUPERFAMILY REMARK 1 REF TRENDS BIOCHEM.SCI. V. 19 5 1994 REMARK 1 REFN ISSN 0968-0004 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.84 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 9649 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-FACTOR REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 934 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1056 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 114 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 : 832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 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) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : INDIVIDUAL RESTRAINED, RMS BONDS 3.5 REMARK 3 A**2 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.000 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.000 ; 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : PARAM3_MOD.CHO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 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 : ELLIOTT GX-21 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA (CCP4), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9843 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 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) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: TWO DERIVATIVES (SMCL3 AND UO2SO4) WERE USED AT 3.0 A REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 67.27000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.31500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 100.90500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.31500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.63500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.31500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 100.90500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.31500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.31500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.63500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 67.27000 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 ALA A -3 REMARK 465 PRO A -2 REMARK 465 LEU A -1 REMARK 465 ARG A 110 REMARK 465 SER A 111 REMARK 465 THR A 112 REMARK 465 HIS A 113 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 50 CD OE1 OE2 REMARK 480 ARG A 96 CZ NH1 NH2 REMARK 480 GLU A 108 CD OE1 OE2 REMARK 480 THR A 114 N CA CB OG1 CG2 DBREF 1BY2 A 1 115 UNP Q08380 LG3BP_HUMAN 19 133 SEQRES 1 A 119 ALA PRO LEU ALA VAL ASN ASP GLY ASP MET ARG LEU ALA SEQRES 2 A 119 ASP GLY GLY ALA THR ASN GLN GLY ARG VAL GLU ILE PHE SEQRES 3 A 119 TYR ARG GLY GLN TRP GLY THR VAL CYS ASP ASN LEU TRP SEQRES 4 A 119 ASP LEU THR ASP ALA SER VAL VAL CYS ARG ALA LEU GLY SEQRES 5 A 119 PHE GLU ASN ALA THR GLN ALA LEU GLY ARG ALA ALA PHE SEQRES 6 A 119 GLY GLN GLY SER GLY PRO ILE MET LEU ASP GLU VAL GLN SEQRES 7 A 119 CYS THR GLY THR GLU ALA SER LEU ALA ASP CYS LYS SER SEQRES 8 A 119 LEU GLY TRP LEU LYS SER ASN CYS ARG HIS GLU ARG ASP SEQRES 9 A 119 ALA GLY VAL VAL CYS THR ASN GLU THR ARG SER THR HIS SEQRES 10 A 119 THR LEU MODRES 1BY2 ASN A 51 ASN GLYCOSYLATION SITE HET NAG A 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 HOH *57(H2 O) HELIX 1 1 LEU A 37 ALA A 46 1 10 HELIX 2 2 LEU A 82 ASP A 84 5 3 HELIX 3 3 HIS A 97 ARG A 99 5 3 SHEET 1 A 4 MET A 6 ALA A 9 0 SHEET 2 A 4 GLN A 16 ILE A 21 -1 N GLU A 20 O ARG A 7 SHEET 3 A 4 GLY A 102 CYS A 105 -1 N VAL A 103 O GLY A 17 SHEET 4 A 4 ALA A 52 LEU A 56 -1 N LEU A 56 O GLY A 102 SHEET 1 B 2 GLU A 20 TYR A 23 0 SHEET 2 B 2 GLN A 26 THR A 29 -1 N GLY A 28 O ILE A 21 SSBOND 1 CYS A 31 CYS A 95 1555 1555 2.02 SSBOND 2 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 3 CYS A 75 CYS A 85 1555 1555 2.02 LINK ND2 ASN A 51 C1 NAG A 201 1555 1555 1.44 CRYST1 44.630 44.630 134.540 90.00 90.00 90.00 P 43 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 0.022406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007433 0.00000