PDB Short entry for 3D34 HEADER IMMUNE SYSTEM 09-MAY-08 3D34 TITLE STRUCTURE OF THE F-SPONDIN DOMAIN OF MINDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPONDIN-2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: F-SPONDIN DOMAIN, UNP RESIDUES 27-249; COMPND 5 SYNONYM: MINDIN, DIFFERENTIALLY EXPRESSED IN CANCEROUS AND COMPND 6 NON-CANCEROUS LUNG CELLS 1, DIL-1; 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: SPON2, DIL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS F-SPONDIN DOMAIN OF MINDIN, CELL ADHESION, EXTRACELLULAR KEYWDS 2 MATRIX, IMMUNE RESPONSE, POLYMORPHISM, SECRETED, IMMUNE KEYWDS 3 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Y.LI,R.A.MARIUZZA REVDAT 1 17-FEB-09 3D34 0 JRNL AUTH Y.LI,C.CAO,W.JIA,L.YU,M.MO,Q.WANG,Y.HUANG,J.M.LIM, JRNL AUTH 2 M.ISHIHARA,L.WELLS,P.AZADI,H.ROBINSON,Y.W.HE, JRNL AUTH 3 L.ZHANG,R.A.MARIUZZA JRNL TITL STRUCTURE OF THE F-SPONDIN DOMAIN OF MINDIN, AN JRNL TITL 2 INTEGRIN LIGAND AND PATTERN RECOGNITION MOLECULE. JRNL REF EMBO J. V. 28 286 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19153605 JRNL DOI 10.1038/EMBOJ.2008.288 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL 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) (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 34285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1757 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 : 3279 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18100 REMARK 3 B22 (A**2) : 0.18500 REMARK 3 B33 (A**2) : -0.00500 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) : 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : 1.095 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.592 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.790 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.565 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 56.50 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:ION.PARAM 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 3D34 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB047531. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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 : SIEMENS 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 : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : DTREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35173 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 3.080 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.96 REMARK 200 R MERGE FOR SHELL (I) : 0.16300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0-6% PEG2000, 100MM TRIS-HCL, 10MM REMARK 280 NICL2, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.30000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.06500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.01350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.06500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.30000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.01350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLN A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 SER A 7 REMARK 465 ARG A 219 REMARK 465 GLN A 220 REMARK 465 SER A 221 REMARK 465 PRO A 222 REMARK 465 ARG A 223 REMARK 465 GLN B 1 REMARK 465 PRO B 2 REMARK 465 LEU B 3 REMARK 465 GLY B 4 REMARK 465 GLY B 5 REMARK 465 GLU B 6 REMARK 465 SER B 7 REMARK 465 ARG B 223 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 ILE A 8 CG1 CG2 CD1 REMARK 470 ARG A 12 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 38 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 ILE B 8 CG1 CG2 CD1 REMARK 470 SER B 10 OG REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 GLU B 113 CG CD OE1 OE2 REMARK 470 ARG B 149 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 205 CG CD CE NZ REMARK 470 ARG B 219 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 220 CG CD OE1 NE2 REMARK 470 SER B 221 OG 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 GLN A 33 CD REMARK 480 PHE A 37 CD2 CE2 REMARK 480 ARG A 59 NH2 REMARK 480 ARG A 69 NE CZ NH1 REMARK 480 GLU A 85 OE1 OE2 REMARK 480 GLU A 89 CD REMARK 480 GLN A 92 CD REMARK 480 GLN A 153 NE2 REMARK 480 ARG A 203 NE REMARK 480 ASP B 148 CB REMARK 480 GLU B 152 OE1 REMARK 480 PHE B 169 CE1 CE2 REMARK 480 PHE B 176 CD1 CE1 CZ REMARK 480 ARG B 217 NH2 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 ASP A 134 43.63 -166.65 REMARK 500 PHE A 176 107.10 -160.37 REMARK 500 ASP B 134 43.36 -161.06 REMARK 500 HIS B 194 138.72 -174.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 465 DISTANCE = 6.85 ANGSTROMS 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 NI A 226 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 16 NZ REMARK 620 2 HOH B 469 O 109.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 225 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 96 OE1 REMARK 620 2 HOH B 469 O 143.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 228 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 134 OD1 REMARK 620 2 ASP A 134 OD2 50.1 REMARK 620 3 ASP A 162 OD1 94.3 80.1 REMARK 620 4 ASP A 162 OD2 81.5 110.1 53.5 REMARK 620 5 ASP A 166 O 85.1 78.6 152.6 152.0 REMARK 620 6 HOH A 242 O 85.8 131.7 128.4 75.7 79.0 REMARK 620 7 HOH A 319 O 155.7 154.3 93.4 84.6 98.4 71.4 REMARK 620 8 HOH A 318 O 130.6 81.1 81.9 128.9 78.0 134.0 73.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 224 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 175 ND2 REMARK 620 2 HOH A 346 O 96.8 REMARK 620 3 HOH A 348 O 150.2 98.9 REMARK 620 4 HOH A 347 O 79.9 161.8 92.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 226 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 134 OD1 REMARK 620 2 ASP B 134 OD2 51.8 REMARK 620 3 ASP B 162 OD1 96.3 77.0 REMARK 620 4 ASP B 162 OD2 86.3 111.2 53.6 REMARK 620 5 ASP B 166 O 84.8 82.1 152.2 153.6 REMARK 620 6 HOH B 361 O 131.0 80.4 80.8 125.8 77.7 REMARK 620 7 HOH B 431 O 155.1 152.8 90.9 79.0 99.7 73.6 REMARK 620 8 HOH B 364 O 82.1 131.3 129.4 75.9 78.3 136.2 75.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 224 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 224 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 225 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 226 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 225 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 228 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 226 DBREF 3D34 A 1 223 UNP Q9BUD6 SPON2_HUMAN 27 249 DBREF 3D34 B 1 223 UNP Q9BUD6 SPON2_HUMAN 27 249 SEQRES 1 A 223 GLN PRO LEU GLY GLY GLU SER ILE CYS SER ALA ARG ALA SEQRES 2 A 223 PRO ALA LYS TYR SER ILE THR PHE THR GLY LYS TRP SER SEQRES 3 A 223 GLN THR ALA PHE PRO LYS GLN TYR PRO LEU PHE ARG PRO SEQRES 4 A 223 PRO ALA GLN TRP SER SER LEU LEU GLY ALA ALA HIS SER SEQRES 5 A 223 SER ASP TYR SER MET TRP ARG LYS ASN GLN TYR VAL SER SEQRES 6 A 223 ASN GLY LEU ARG ASP PHE ALA GLU ARG GLY GLU ALA TRP SEQRES 7 A 223 ALA LEU MET LYS GLU ILE GLU ALA ALA GLY GLU ALA LEU SEQRES 8 A 223 GLN SER VAL HIS GLU VAL PHE SER ALA PRO ALA VAL PRO SEQRES 9 A 223 SER GLY THR GLY GLN THR SER ALA GLU LEU GLU VAL GLN SEQRES 10 A 223 ARG ARG HIS SER LEU VAL SER PHE VAL VAL ARG ILE VAL SEQRES 11 A 223 PRO SER PRO ASP TRP PHE VAL GLY VAL ASP SER LEU ASP SEQRES 12 A 223 LEU CYS ASP GLY ASP ARG TRP ARG GLU GLN ALA ALA LEU SEQRES 13 A 223 ASP LEU TYR PRO TYR ASP ALA GLY THR ASP SER GLY PHE SEQRES 14 A 223 THR PHE SER SER PRO ASN PHE ALA THR ILE PRO GLN ASP SEQRES 15 A 223 THR VAL THR GLU ILE THR SER SER SER PRO SER HIS PRO SEQRES 16 A 223 ALA ASN SER PHE TYR TYR PRO ARG LEU LYS ALA LEU PRO SEQRES 17 A 223 PRO ILE ALA ARG VAL THR LEU LEU ARG LEU ARG GLN SER SEQRES 18 A 223 PRO ARG SEQRES 1 B 223 GLN PRO LEU GLY GLY GLU SER ILE CYS SER ALA ARG ALA SEQRES 2 B 223 PRO ALA LYS TYR SER ILE THR PHE THR GLY LYS TRP SER SEQRES 3 B 223 GLN THR ALA PHE PRO LYS GLN TYR PRO LEU PHE ARG PRO SEQRES 4 B 223 PRO ALA GLN TRP SER SER LEU LEU GLY ALA ALA HIS SER SEQRES 5 B 223 SER ASP TYR SER MET TRP ARG LYS ASN GLN TYR VAL SER SEQRES 6 B 223 ASN GLY LEU ARG ASP PHE ALA GLU ARG GLY GLU ALA TRP SEQRES 7 B 223 ALA LEU MET LYS GLU ILE GLU ALA ALA GLY GLU ALA LEU SEQRES 8 B 223 GLN SER VAL HIS GLU VAL PHE SER ALA PRO ALA VAL PRO SEQRES 9 B 223 SER GLY THR GLY GLN THR SER ALA GLU LEU GLU VAL GLN SEQRES 10 B 223 ARG ARG HIS SER LEU VAL SER PHE VAL VAL ARG ILE VAL SEQRES 11 B 223 PRO SER PRO ASP TRP PHE VAL GLY VAL ASP SER LEU ASP SEQRES 12 B 223 LEU CYS ASP GLY ASP ARG TRP ARG GLU GLN ALA ALA LEU SEQRES 13 B 223 ASP LEU TYR PRO TYR ASP ALA GLY THR ASP SER GLY PHE SEQRES 14 B 223 THR PHE SER SER PRO ASN PHE ALA THR ILE PRO GLN ASP SEQRES 15 B 223 THR VAL THR GLU ILE THR SER SER SER PRO SER HIS PRO SEQRES 16 B 223 ALA ASN SER PHE TYR TYR PRO ARG LEU LYS ALA LEU PRO SEQRES 17 B 223 PRO ILE ALA ARG VAL THR LEU LEU ARG LEU ARG GLN SER SEQRES 18 B 223 PRO ARG HET NI A 224 1 HET NI A 225 1 HET NI A 226 1 HET NI A 227 1 HET CA A 228 1 HET NI B 224 1 HET NI B 225 1 HET CA B 226 1 HETNAM NI NICKEL (II) ION HETNAM CA CALCIUM ION FORMUL 3 NI 6(NI 2+) FORMUL 7 CA 2(CA 2+) FORMUL 11 HOH *319(H2 O) HELIX 1 1 SER A 65 GLY A 75 1 11 HELIX 2 2 ALA A 77 GLN A 92 1 16 HELIX 3 3 SER B 65 GLY B 75 1 11 HELIX 4 4 ALA B 77 GLN B 92 1 16 SHEET 1 A 4 GLN A 109 VAL A 116 0 SHEET 2 A 4 ALA A 15 GLY A 23 -1 N PHE A 21 O THR A 110 SHEET 3 A 4 ALA A 211 ARG A 217 -1 O ARG A 212 N THR A 22 SHEET 4 A 4 GLN A 153 LEU A 158 -1 N ALA A 154 O LEU A 215 SHEET 1 B 6 VAL A 94 ALA A 100 0 SHEET 2 B 6 GLN A 42 HIS A 51 -1 N GLY A 48 O PHE A 98 SHEET 3 B 6 LEU A 122 VAL A 130 -1 O VAL A 130 N GLN A 42 SHEET 4 B 6 TRP A 135 ASP A 143 -1 O LEU A 142 N VAL A 123 SHEET 5 B 6 TYR A 161 ASP A 162 -1 O TYR A 161 N PHE A 136 SHEET 6 B 6 THR A 185 GLU A 186 -1 O THR A 185 N ASP A 162 SHEET 1 C 2 CYS A 145 ASP A 146 0 SHEET 2 C 2 ARG A 149 TRP A 150 -1 O ARG A 149 N ASP A 146 SHEET 1 D 4 THR B 107 VAL B 116 0 SHEET 2 D 4 ALA B 15 LYS B 24 -1 N GLY B 23 O GLY B 108 SHEET 3 D 4 ALA B 211 ARG B 217 -1 O ARG B 212 N THR B 22 SHEET 4 D 4 GLN B 153 LEU B 158 -1 N LEU B 158 O ALA B 211 SHEET 1 E 4 GLN B 42 TRP B 43 0 SHEET 2 E 4 LEU B 122 VAL B 130 -1 O VAL B 130 N GLN B 42 SHEET 3 E 4 LEU B 46 HIS B 51 -1 N HIS B 51 O LEU B 122 SHEET 4 E 4 VAL B 94 ALA B 100 -1 O PHE B 98 N GLY B 48 SHEET 1 F 5 GLN B 42 TRP B 43 0 SHEET 2 F 5 LEU B 122 VAL B 130 -1 O VAL B 130 N GLN B 42 SHEET 3 F 5 TRP B 135 ASP B 143 -1 O LEU B 142 N VAL B 123 SHEET 4 F 5 TYR B 161 ASP B 162 -1 O TYR B 161 N PHE B 136 SHEET 5 F 5 THR B 185 GLU B 186 -1 O THR B 185 N ASP B 162 SHEET 1 G 2 CYS B 145 ASP B 146 0 SHEET 2 G 2 ARG B 149 TRP B 150 -1 O ARG B 149 N ASP B 146 SSBOND 1 CYS A 9 CYS A 145 1555 1555 2.03 SSBOND 2 CYS B 9 CYS B 145 1555 1555 2.03 LINK NZ LYS A 16 NI NI A 226 1555 1555 2.55 LINK OE1 GLU A 96 NI NI A 225 1555 1555 2.52 LINK OD1 ASP A 134 CA CA A 228 1555 1555 2.56 LINK OD2 ASP A 134 CA CA A 228 1555 1555 2.62 LINK OD1 ASP A 162 CA CA A 228 1555 1555 2.47 LINK OD2 ASP A 162 CA CA A 228 1555 1555 2.41 LINK O ASP A 166 CA CA A 228 1555 1555 2.30 LINK ND2 ASN A 175 NI NI A 224 1555 1555 2.05 LINK NZ LYS B 16 NI NI B 224 1555 1555 2.03 LINK OD1 ASP B 134 CA CA B 226 1555 1555 2.50 LINK OD2 ASP B 134 CA CA B 226 1555 1555 2.50 LINK OD1 ASP B 162 CA CA B 226 1555 1555 2.49 LINK OD2 ASP B 162 CA CA B 226 1555 1555 2.37 LINK O ASP B 166 CA CA B 226 1555 1555 2.36 LINK NI NI A 224 O HOH A 346 1555 1555 2.14 LINK NI NI A 224 O HOH A 348 1555 1555 2.04 LINK NI NI A 224 O HOH A 347 1555 1555 2.09 LINK NI NI A 225 O HOH B 469 1555 1555 2.28 LINK NI NI A 226 O HOH B 469 1555 1555 2.39 LINK CA CA A 228 O HOH A 242 1555 1555 2.60 LINK CA CA A 228 O HOH A 319 1555 1555 2.49 LINK CA CA A 228 O HOH A 318 1555 1555 2.48 LINK NI NI B 225 O HOH B 469 1555 1555 2.26 LINK CA CA B 226 O HOH B 361 1555 1555 2.54 LINK CA CA B 226 O HOH B 431 1555 1555 2.57 LINK CA CA B 226 O HOH B 364 1555 1555 2.46 CISPEP 1 ARG A 38 PRO A 39 0 -0.12 CISPEP 2 VAL A 130 PRO A 131 0 -0.27 CISPEP 3 ILE A 179 PRO A 180 0 -0.26 CISPEP 4 SER A 191 PRO A 192 0 0.13 CISPEP 5 ARG B 38 PRO B 39 0 0.00 CISPEP 6 VAL B 130 PRO B 131 0 -0.14 CISPEP 7 ILE B 179 PRO B 180 0 -0.02 CISPEP 8 SER B 191 PRO B 192 0 0.35 SITE 1 AC1 1 ASN A 175 SITE 1 AC2 1 LYS B 16 SITE 1 AC3 1 GLU A 96 SITE 1 AC4 1 LYS A 16 SITE 1 AC5 2 LYS B 16 GLU B 96 SITE 1 AC7 3 ASP A 134 ASP A 162 ASP A 166 SITE 1 AC8 3 ASP B 134 ASP B 162 ASP B 166 CRYST1 50.600 68.027 110.130 90.00 90.00 90.00 P 21 21 21 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 0.019763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009080 0.00000