HEADER CELL ADHESION 04-AUG-17 5Y4M TITLE DISCOIDIN DOMAIN OF HUMAN CASPR2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN CASPR2 DISC DOMAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CONTACTIN-ASSOCIATED PROTEIN-LIKE 2; COMPND 5 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: CNTNAP2, CASPR2, KIAA0868; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS EPITOPE FOR AUTOANTIBODY, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR H.LIU,F.XU,J.ZHANG,W.LIANG REVDAT 2 20-FEB-19 5Y4M 1 JRNL REVDAT 1 08-AUG-18 5Y4M 0 JRNL AUTH W.LIANG,J.ZHANG,M.SAINT-MARTIN,F.XU,N.NORAZ,J.LIU, JRNL AUTH 2 J.HONNORAT,H.LIU JRNL TITL STRUCTURAL MAPPING OF HOT SPOTS WITHIN HUMAN CASPR2 JRNL TITL 2 DISCOIDIN DOMAIN FOR AUTOANTIBODY RECOGNITION. JRNL REF J. AUTOIMMUN. V. 96 168 2019 JRNL REFN ISSN 1095-9157 JRNL PMID 30337146 JRNL DOI 10.1016/J.JAUT.2018.09.012 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 33331 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1586 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 43.2187 - 2.9102 0.99 3045 150 0.1433 0.1594 REMARK 3 2 2.9102 - 2.3100 1.00 2945 136 0.1516 0.1916 REMARK 3 3 2.3100 - 2.0180 1.00 2900 149 0.1276 0.1512 REMARK 3 4 2.0180 - 1.8335 1.00 2898 156 0.1229 0.1676 REMARK 3 5 1.8335 - 1.7020 1.00 2893 120 0.1137 0.1370 REMARK 3 6 1.7020 - 1.6017 1.00 2892 141 0.1190 0.1521 REMARK 3 7 1.6017 - 1.5215 1.00 2821 164 0.1234 0.1651 REMARK 3 8 1.5215 - 1.4552 1.00 2831 167 0.1263 0.1665 REMARK 3 9 1.4552 - 1.3992 1.00 2863 140 0.1341 0.1847 REMARK 3 10 1.3992 - 1.3509 1.00 2878 128 0.1481 0.2079 REMARK 3 11 1.3509 - 1.3087 0.98 2779 135 0.1724 0.2171 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.240 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 : 0.005 1246 REMARK 3 ANGLE : 0.858 1695 REMARK 3 CHIRALITY : 0.084 167 REMARK 3 PLANARITY : 0.005 222 REMARK 3 DIHEDRAL : 24.627 454 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5Y4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1300004339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8-6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33381 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 35.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53800 REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 FOR SHELL : 2.750 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG8000,100 MM NA2HPO4/KH2PO4, PH REMARK 280 6.2, 200 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 296K 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 18.12500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.29950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.29950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.12500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.84000 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 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 30 REMARK 465 PRO A 31 REMARK 465 GLY A 32 REMARK 465 ASP A 33 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 322 O HOH A 451 2.09 REMARK 500 O HOH A 373 O HOH A 436 2.18 REMARK 500 O HOH A 466 O HOH A 491 2.19 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 ASP A 36 31.43 -153.75 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 A 507 DISTANCE = 6.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 DBREF 5Y4M A 35 181 UNP Q9UHC6 CNTP2_HUMAN 35 181 SEQADV 5Y4M ALA A 30 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M PRO A 31 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M GLY A 32 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M ASP A 33 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M PRO A 34 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M ALA A 182 UNP Q9UHC6 EXPRESSION TAG SEQADV 5Y4M ALA A 183 UNP Q9UHC6 EXPRESSION TAG SEQRES 1 A 154 ALA PRO GLY ASP PRO CYS ASP GLU PRO LEU VAL SER GLY SEQRES 2 A 154 LEU PRO HIS VAL ALA PHE SER SER SER SER SER ILE SER SEQRES 3 A 154 GLY SER TYR SER PRO GLY TYR ALA LYS ILE ASN LYS ARG SEQRES 4 A 154 GLY GLY ALA GLY GLY TRP SER PRO SER ASP SER ASP HIS SEQRES 5 A 154 TYR GLN TRP LEU GLN VAL ASP PHE GLY ASN ARG LYS GLN SEQRES 6 A 154 ILE SER ALA ILE ALA THR GLN GLY ARG TYR SER SER SER SEQRES 7 A 154 ASP TRP VAL THR GLN TYR ARG MET LEU TYR SER ASP THR SEQRES 8 A 154 GLY ARG ASN TRP LYS PRO TYR HIS GLN ASP GLY ASN ILE SEQRES 9 A 154 TRP ALA PHE PRO GLY ASN ILE ASN SER ASP GLY VAL VAL SEQRES 10 A 154 ARG HIS GLU LEU GLN HIS PRO ILE ILE ALA ARG TYR VAL SEQRES 11 A 154 ARG ILE VAL PRO LEU ASP TRP ASN GLY GLU GLY ARG ILE SEQRES 12 A 154 GLY LEU ARG ILE GLU VAL TYR GLY CYS ALA ALA HET EDO A 201 4 HET EDO A 202 4 HET EDO A 203 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 5 HOH *207(H2 O) HELIX 1 AA1 PRO A 44 VAL A 46 5 3 HELIX 2 AA2 SER A 55 ALA A 63 5 9 SHEET 1 AA1 6 GLU A 37 PRO A 38 0 SHEET 2 AA1 6 ARG A 175 ALA A 182 -1 O GLY A 180 N GLU A 37 SHEET 3 AA1 6 LEU A 85 GLN A 101 -1 N SER A 96 O TYR A 179 SHEET 4 AA1 6 VAL A 146 TRP A 166 -1 O HIS A 148 N ILE A 98 SHEET 5 AA1 6 VAL A 110 SER A 118 -1 N GLN A 112 O LEU A 164 SHEET 6 AA1 6 LYS A 125 PRO A 126 -1 O LYS A 125 N TYR A 117 SHEET 1 AA2 5 PHE A 48 SER A 50 0 SHEET 2 AA2 5 LEU A 85 GLN A 101 -1 O GLN A 86 N SER A 49 SHEET 3 AA2 5 VAL A 146 TRP A 166 -1 O HIS A 148 N ILE A 98 SHEET 4 AA2 5 VAL A 110 SER A 118 -1 N GLN A 112 O LEU A 164 SHEET 5 AA2 5 PHE A 136 PRO A 137 -1 O PHE A 136 N TYR A 113 SHEET 1 AA3 2 HIS A 128 GLN A 129 0 SHEET 2 AA3 2 ASN A 132 ILE A 133 -1 O ASN A 132 N GLN A 129 SSBOND 1 CYS A 35 CYS A 181 1555 1555 2.04 SITE 1 AC1 3 ASP A 165 TRP A 166 HOH A 415 SITE 1 AC2 5 HIS A 45 GLY A 61 LYS A 64 HOH A 310 SITE 2 AC2 5 HOH A 381 SITE 1 AC3 5 GLU A 149 ARG A 160 HOH A 328 HOH A 413 SITE 2 AC3 5 HOH A 417 CRYST1 36.250 59.680 62.599 90.00 90.00 90.00 P 21 21 21 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 0.027586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015975 0.00000