HEADER CELL ADHESION 30-AUG-07 2VA4 OBSLTE 23-FEB-11 2VA4 2XY1 TITLE CRYSTAL STRUCTURE OF NCAM2 IG34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL CELL ADHESION MOLECULE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG34, RESIDUES 209-398; COMPND 5 SYNONYM: NCAM2, N-CAM 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; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: KM71H; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PPICZALFAC; SOURCE 9 OTHER_DETAILS: RECOMBINANT KEYWDS TRANSMEMBRANE, PHOSPHORYLATION, IMMUNOGLOBULIN DOMAIN, KEYWDS 2 MEMBRANE, ADHESION, GLYCOPROTEIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.KULAHIN,K.K.RASMUSSEN,O.KRISTENSEN,V.BEREZIN,E.BOCK, AUTHOR 2 P.WALMOD,M.GAJHEDE REVDAT 3 23-FEB-11 2VA4 1 OBSLTE REVDAT 2 24-FEB-09 2VA4 1 VERSN REVDAT 1 23-SEP-08 2VA4 0 JRNL AUTH N.KULAHIN,K.K.RASMUSSEN,O.KRISTENSEN,V.BEREZIN, JRNL AUTH 2 E.BOCK,P.WALMOD,M.GAJHEDE JRNL TITL CRYSTAL STRUCTURE OF NCAM2 IG34 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.9 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.9 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 13110 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.2141 REMARK 3 R VALUE (WORKING SET) : 0.2048 REMARK 3 FREE R VALUE : 0.2952 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5 REMARK 3 FREE R VALUE TEST SET COUNT : 655 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 2VA4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-AUG-07. REMARK 100 THE PDBE ID CODE IS EBI-33623. 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) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24902 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.90 REMARK 200 RESOLUTION RANGE LOW (A) : 20.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 1.6 REMARK 200 R MERGE (I) : 0.16 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.68 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.24 REMARK 200 R MERGE FOR SHELL (I) : 0.66 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.99 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 (%): 45.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG-6000, 0.1 M HEPES REMARK 280 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 22.90000 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 GENERATING THE BIOMOLECULE 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: PQS 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 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 ND2 ASN A 309 - O5 NAG A 402 2.06 REMARK 500 ND2 ASN A 309 - C2 NAG A 402 1.88 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 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 223 11.16 58.19 REMARK 500 ASN A 254 -152.94 -143.09 REMARK 500 THR A 344 -158.93 -123.49 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 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 402 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- REMARK 900 III DOMAIN OFHUMAN NEURAL CELL ADHESION REMARK 900 MOLECULE 2 REMARK 900 RELATED ID: 2V44 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 REMARK 900 UNIT) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS A 2 AMINO ACID DIFFERENCE BETWEEN THE PROTEIN REMARK 999 SEQUENCE AND DATABASE SEQUENCE. THE SEQUENCE DESCRIBED REMARK 999 CORRESPONDS TO THE SEQUENCE OF THE PROTEIN AS ANNOTATED REMARK 999 IN THE ENSEMBL DATABASE. DBREF 2VA4 A 207 208 PDB 2VA4 2VA4 207 208 DBREF 2VA4 A 209 398 UNP O15394 NCAM2_HUMAN 209 398 SEQADV 2VA4 LEU A 350 UNP O15394 PRO 350 CONFLICT SEE REMARK 999 SEQADV 2VA4 ASP A 374 UNP O15394 GLY 374 CONFLICT SEE REMARK 999 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 HET NAG A 401 14 HET NAG A 402 14 HETNAM NAG N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 HOH *99(H2 O1) 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 5 SER A 217 THR A 221 0 SHEET 2 AB 5 GLY A 288 LEU A 307 1 O PHE A 295 N PHE A 218 SHEET 3 AB 5 GLY A 277 ASN A 285 -1 O GLY A 277 N LEU A 296 SHEET 4 AB 5 ALA A 241 ARG A 246 -1 O ALA A 241 N THR A 284 SHEET 5 AB 5 LYS A 249 LEU A 250 -1 O LYS A 249 N ARG A 246 SHEET 1 AC 2 SER A 217 THR A 221 0 SHEET 2 AC 2 GLY A 288 LEU A 307 1 O PHE A 295 N PHE A 218 SHEET 1 AD 3 MET A 228 SER A 231 0 SHEET 2 AD 3 GLU A 265 VAL A 268 -1 O LEU A 266 N PHE A 230 SHEET 3 AD 3 TYR A 257 LYS A 260 -1 O ILE A 258 N THR A 267 SHEET 1 AE 5 GLU A 310 THR A 312 0 SHEET 2 AE 5 GLY A 388 ILE A 397 1 O TYR A 394 N GLU A 310 SHEET 3 AE 5 GLY A 376 ALA A 383 -1 O GLY A 376 N LEU A 395 SHEET 4 AE 5 GLU A 331 ARG A 336 -1 O GLU A 331 N ALA A 383 SHEET 5 AE 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 2.03 LINK ND2 ASN A 219 C1 NAG A 401 1555 1555 1.45 LINK ND2 ASN A 309 C1 NAG A 402 1555 1555 1.45 CISPEP 1 SER A 237 PRO A 238 0 2.38 CISPEP 2 GLU A 327 PRO A 328 0 4.00 CISPEP 3 GLU A 345 GLY A 346 0 -5.27 SITE 1 AC1 5 ASN A 219 GLN A 317 THR A 319 ARG A 385 SITE 2 AC1 5 HOH A2099 SITE 1 AC2 2 ASN A 309 TYR A 394 CRYST1 43.900 45.800 46.100 90.00 103.20 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 0.022779 0.000000 0.005343 0.00000 SCALE2 0.000000 0.021834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022281 0.00000