HEADER CELL ADHESION 12-NOV-10 2XY1 TITLE CRYSTAL STRUCTURE OF NCAM2 IG3-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL CELL ADHESION MOLECULE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG3-4, RESIDUES 209-398; COMPND 5 SYNONYM: NCAM2, 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 2 29-JUL-20 2XY1 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 23-FEB-11 2XY1 0 SPRSDE 23-FEB-11 2XY1 2VA4 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. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 12014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 572 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 19.9940 - 3.1381 0.98 2959 153 0.1779 0.2298 REMARK 3 2 3.1381 - 2.4923 0.98 2907 143 0.2048 0.3135 REMARK 3 3 2.4923 - 2.1777 0.95 2775 144 0.2467 0.3100 REMARK 3 4 2.1777 - 1.9788 0.95 2801 132 0.2400 0.2883 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 41.64 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.07550 REMARK 3 B22 (A**2) : 4.45010 REMARK 3 B33 (A**2) : 4.62550 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 11.75690 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 1592 REMARK 3 ANGLE : 1.149 2155 REMARK 3 CHIRALITY : 0.075 237 REMARK 3 PLANARITY : 0.004 283 REMARK 3 DIHEDRAL : 14.482 618 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 2XY1 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_1290046060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : XIA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 20.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 41.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-6000, 0.1 M HEPES PH7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 22.90500 REMARK 290 SMTRY3 2 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OH TYR A 313 NH1 ARG A 385 1655 2.12 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 ASN A 254 -153.40 -157.35 REMARK 500 THR A 344 -168.46 -122.11 REMARK 500 GLU A 345 -131.13 59.51 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: 2XY2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG1-2 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: 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: 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 DBREF 2XY1 A 209 398 UNP O15394 NCAM2_HUMAN 209 398 SEQADV 2XY1 SER A 207 UNP O15394 EXPRESSION TAG SEQADV 2XY1 MET A 208 UNP O15394 EXPRESSION TAG SEQRES 1 A 192 SER MET PRO ALA ILE SER MET PRO GLN LYS SER PHE ASN SEQRES 2 A 192 ALA THR ALA GLU ARG GLY GLU GLU MET THR PHE SER CYS SEQRES 3 A 192 ARG ALA SER GLY SER PRO GLU PRO ALA ILE SER TRP PHE SEQRES 4 A 192 ARG ASN GLY LYS LEU ILE GLU GLU ASN GLU LYS TYR ILE SEQRES 5 A 192 LEU LYS GLY SER ASN THR GLU LEU THR VAL ARG ASN ILE SEQRES 6 A 192 ILE ASN SER ASP GLY GLY PRO TYR VAL CYS ARG ALA THR SEQRES 7 A 192 ASN LYS ALA GLY GLU ASP GLU LYS GLN ALA PHE LEU GLN SEQRES 8 A 192 VAL PHE VAL GLN PRO HIS ILE ILE GLN LEU LYS ASN GLU SEQRES 9 A 192 THR THR TYR GLU ASN GLY GLN VAL THR LEU VAL CYS ASP SEQRES 10 A 192 ALA GLU GLY GLU PRO ILE PRO GLU ILE THR TRP LYS ARG SEQRES 11 A 192 ALA VAL ASP GLY PHE THR PHE THR GLU GLY ASP LYS SER SEQRES 12 A 192 LEU ASP GLY ARG ILE GLU VAL LYS GLY GLN HIS GLY SER SEQRES 13 A 192 SER SER LEU HIS ILE LYS ASP VAL LYS LEU SER ASP SER SEQRES 14 A 192 GLY ARG TYR ASP CYS GLU ALA ALA SER ARG ILE GLY GLY SEQRES 15 A 192 HIS GLN LYS SER MET TYR LEU ASP ILE GLU MODRES 2XY1 ASN A 219 ASN GLYCOSYLATION SITE MODRES 2XY1 ASN A 309 ASN GLYCOSYLATION SITE HET NAG A 401 14 HET NAG A 402 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 4 HOH *93(H2 O) HELIX 1 1 ILE A 272 GLY A 276 5 5 HELIX 2 2 LYS A 371 SER A 375 5 5 SHEET 1 AA 2 ALA A 210 SER A 212 0 SHEET 2 AA 2 ARG A 233 SER A 235 -1 O ARG A 233 N SER A 212 SHEET 1 AB 2 SER A 217 THR A 221 0 SHEET 2 AB 2 GLY A 288 LEU A 307 1 O PHE A 295 N PHE A 218 SHEET 1 AC 7 LYS A 249 LEU A 250 0 SHEET 2 AC 7 ALA A 241 ARG A 246 -1 O ARG A 246 N LYS A 249 SHEET 3 AC 7 GLY A 277 ASN A 285 -1 O VAL A 280 N PHE A 245 SHEET 4 AC 7 GLY A 288 LEU A 307 -1 O GLY A 288 N ASN A 285 SHEET 5 AC 7 GLN A 317 GLU A 327 -1 O ASP A 323 N ILE A 305 SHEET 6 AC 7 SER A 362 LYS A 368 -1 O SER A 363 N CYS A 322 SHEET 7 AC 7 ILE A 354 GLN A 359 -1 O GLU A 355 N HIS A 366 SHEET 1 AD 5 LYS A 249 LEU A 250 0 SHEET 2 AD 5 ALA A 241 ARG A 246 -1 O ARG A 246 N LYS A 249 SHEET 3 AD 5 GLY A 277 ASN A 285 -1 O VAL A 280 N PHE A 245 SHEET 4 AD 5 GLY A 288 LEU A 307 -1 O GLY A 288 N ASN A 285 SHEET 5 AD 5 SER A 217 THR A 221 1 O PHE A 218 N GLN A 297 SHEET 1 AE 3 MET A 228 SER A 231 0 SHEET 2 AE 3 GLU A 265 VAL A 268 -1 O LEU A 266 N PHE A 230 SHEET 3 AE 3 TYR A 257 LYS A 260 -1 O ILE A 258 N THR A 267 SHEET 1 AF 5 GLU A 310 THR A 312 0 SHEET 2 AF 5 GLY A 387 ILE A 397 1 O TYR A 394 N GLU A 310 SHEET 3 AF 5 GLY A 376 SER A 384 -1 O GLY A 376 N LEU A 395 SHEET 4 AF 5 GLU A 331 ARG A 336 -1 O GLU A 331 N ALA A 383 SHEET 5 AF 5 PHE A 341 PHE A 343 -1 O PHE A 341 N ARG A 336 SSBOND 1 CYS A 232 CYS A 281 1555 1555 2.02 SSBOND 2 CYS A 322 CYS A 380 1555 1555 2.02 LINK ND2 ASN A 219 C1 NAG A 401 1555 1555 1.44 LINK ND2 ASN A 309 C1 NAG A 402 1555 1555 1.44 CISPEP 1 SER A 237 PRO A 238 0 -1.51 CISPEP 2 GLU A 327 PRO A 328 0 3.33 CISPEP 3 GLU A 345 GLY A 346 0 -5.87 CRYST1 43.810 45.810 45.720 90.00 103.58 90.00 P 1 21 1 2 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 0.022826 0.000000 0.005514 0.00000 SCALE2 0.000000 0.021829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022501 0.00000