HEADER CELL ADHESION 12-NOV-10 2XY2 TITLE CRYSTAL STRUCTURE OF NCAM2 IG1-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL CELL ADHESION MOLECULE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG1-2, RESIDUES 19-207; COMPND 5 SYNONYM: N-CAM-2, NCAM-2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.KULAHIN,K.K.RASMUSSEN,O.KRISTENSEN,V.BEREZIN,E.BOCK,P.S.WALMOD, AUTHOR 2 M.GAJHEDE REVDAT 3 29-JUL-20 2XY2 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 17-JAN-18 2XY2 1 REMARK REVDAT 1 23-FEB-11 2XY2 0 SPRSDE 23-FEB-11 2XY2 2V44 JRNL AUTH N.KULAHIN,O.KRISTENSEN,K.K.RASMUSSEN,L.OLSEN,P.RYDBERG, JRNL AUTH 2 B.VESTERGAARD,J.S.KASTRUP,V.BEREZIN,E.BOCK,P.S.WALMOD, JRNL AUTH 3 M.GAJHEDE JRNL TITL STRUCTURAL MODEL AND TRANS-INTERACTION OF THE ENTIRE JRNL TITL 2 ECTODOMAIN OF THE OLFACTORY CELL ADHESION MOLECULE. JRNL REF STRUCTURE V. 19 203 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21300289 JRNL DOI 10.1016/J.STR.2010.12.014 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19487 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 984 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 24.7858 - 3.4831 0.98 2816 137 0.1974 0.1931 REMARK 3 2 3.4831 - 2.7658 1.00 2718 131 0.1849 0.2519 REMARK 3 3 2.7658 - 2.4165 1.00 2649 139 0.2094 0.2823 REMARK 3 4 2.4165 - 2.1957 1.00 2630 133 0.2205 0.2689 REMARK 3 5 2.1957 - 2.0384 1.00 2615 145 0.2108 0.2751 REMARK 3 6 2.0384 - 1.9183 1.00 2557 143 0.2242 0.2781 REMARK 3 7 1.9183 - 1.8222 0.98 2518 156 0.2752 0.3288 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 : 0.40 REMARK 3 B_SOL : 64.79 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.300 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) : 1.91020 REMARK 3 B22 (A**2) : 1.91020 REMARK 3 B33 (A**2) : -3.82050 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 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 : 0.007 1546 REMARK 3 ANGLE : 1.052 2095 REMARK 3 CHIRALITY : 0.072 244 REMARK 3 PLANARITY : 0.004 273 REMARK 3 DIHEDRAL : 16.375 581 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 2XY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1290045861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.907 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH SX-165 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XIA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 28.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG-4000, 0.2 M SODIUM ACETATE REMARK 280 TRIHYDRATE, 0.1 M TRIS HYDROCHLORIDE PH 8.5. 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 67.63667 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 135.27333 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 135.27333 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 67.63667 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2066 LIES ON A SPECIAL POSITION. 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 OG SER A 26 O HOH A 2004 2.09 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 GLU A 119 63.82 32.07 REMARK 500 ASN A 152 -112.01 -140.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V5T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG2-3 REMARK 900 RELATED ID: 2DOC RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE FIBRONECTIN TYPE-III DOMAIN OFHUMAN REMARK 900 NEURAL CELL ADHESION MOLECULE 2 REMARK 900 RELATED ID: 2VAJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG1 (I4122 CELL UNIT) REMARK 900 RELATED ID: 2JLL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3II REMARK 900 RELATED ID: 2XYC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IGIV-FN3I REMARK 900 RELATED ID: 2WIM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG1-3 REMARK 900 RELATED ID: 2XY1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG3-4 DBREF 2XY2 A 19 207 UNP O15394 NCAM2_HUMAN 19 207 SEQRES 1 A 189 ALA LEU LEU GLN VAL THR ILE SER LEU SER LYS VAL GLU SEQRES 2 A 189 LEU SER VAL GLY GLU SER LYS PHE PHE THR CYS THR ALA SEQRES 3 A 189 ILE GLY GLU PRO GLU SER ILE ASP TRP TYR ASN PRO GLN SEQRES 4 A 189 GLY GLU LYS ILE ILE SER THR GLN ARG VAL VAL VAL GLN SEQRES 5 A 189 LYS GLU GLY VAL ARG SER ARG LEU THR ILE TYR ASN ALA SEQRES 6 A 189 ASN ILE GLU ASP ALA GLY ILE TYR ARG CYS GLN ALA THR SEQRES 7 A 189 ASP ALA LYS GLY GLN THR GLN GLU ALA THR VAL VAL LEU SEQRES 8 A 189 GLU ILE TYR GLN LYS LEU THR PHE ARG GLU VAL VAL SER SEQRES 9 A 189 PRO GLN GLU PHE LYS GLN GLY GLU ASP ALA GLU VAL VAL SEQRES 10 A 189 CYS ARG VAL SER SER SER PRO ALA PRO ALA VAL SER TRP SEQRES 11 A 189 LEU TYR HIS ASN GLU GLU VAL THR THR ILE SER ASP ASN SEQRES 12 A 189 ARG PHE ALA MET LEU ALA ASN ASN ASN LEU GLN ILE LEU SEQRES 13 A 189 ASN ILE ASN LYS SER ASP GLU GLY ILE TYR ARG CYS GLU SEQRES 14 A 189 GLY ARG VAL GLU ALA ARG GLY GLU ILE ASP PHE ARG ASP SEQRES 15 A 189 ILE ILE VAL ILE VAL ASN VAL MODRES 2XY2 ASN A 177 ASN GLYCOSYLATION SITE HET NAG A1208 14 HET GOL A1209 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG C8 H15 N O6 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *175(H2 O) HELIX 1 1 ASN A 84 ALA A 88 5 5 HELIX 2 2 ASN A 177 GLU A 181 5 5 SHEET 1 AA 4 LEU A 20 ILE A 25 0 SHEET 2 AA 4 LYS A 38 GLY A 46 -1 O THR A 43 N THR A 24 SHEET 3 AA 4 ARG A 75 ILE A 80 -1 O SER A 76 N CYS A 42 SHEET 4 AA 4 VAL A 67 GLU A 72 -1 O VAL A 68 N THR A 79 SHEET 1 AB 4 LYS A 29 SER A 33 0 SHEET 2 AB 4 THR A 102 TYR A 112 1 O VAL A 108 N VAL A 30 SHEET 3 AB 4 GLY A 89 THR A 96 -1 O GLY A 89 N LEU A 109 SHEET 4 AB 4 SER A 50 TYR A 54 -1 O SER A 50 N THR A 96 SHEET 1 AC 2 THR A 116 PHE A 117 0 SHEET 2 AC 2 VAL A 138 SER A 139 -1 O SER A 139 N THR A 116 SHEET 1 AD 5 GLN A 124 LYS A 127 0 SHEET 2 AD 5 GLU A 195 ASN A 206 1 O ILE A 202 N GLN A 124 SHEET 3 AD 5 GLY A 182 VAL A 190 -1 O GLY A 182 N VAL A 203 SHEET 4 AD 5 ALA A 145 TYR A 150 -1 O ALA A 145 N ARG A 189 SHEET 5 AD 5 THR A 156 THR A 157 -1 O THR A 156 N TYR A 150 SHEET 1 AE 3 ALA A 132 VAL A 134 0 SHEET 2 AE 3 LEU A 171 ILE A 173 -1 O LEU A 171 N VAL A 134 SHEET 3 AE 3 PHE A 163 MET A 165 -1 O ALA A 164 N GLN A 172 SSBOND 1 CYS A 42 CYS A 93 1555 1555 2.02 SSBOND 2 CYS A 136 CYS A 186 1555 1555 2.03 LINK ND2 ASN A 177 C1 NAG A1208 1555 1555 1.44 CISPEP 1 SER A 122 PRO A 123 0 2.58 CISPEP 2 SER A 141 PRO A 142 0 -3.02 CRYST1 42.060 42.060 202.910 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 0.023776 0.013727 0.000000 0.00000 SCALE2 0.000000 0.027454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004928 0.00000