HEADER CELL ADHESION 27-JUN-07 2V44 OBSLTE 23-FEB-11 2V44 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: NCAM2; 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_PLASMID: PPICZALFAC KEYWDS CELL ADHESION, PHOSPHORYLATION, IMMUNOGLOBULIN DOMAIN, KEYWDS 2 NEURAL CELL ADHESION MOLECULE, IG, NCAM2, MEMBRANE, KEYWDS 3 HOMPHILIC, GLYCOPROTEIN, TRANSMEMBRANE, IMMUNOGLOBULIN EXPDTA X-RAY DIFFRACTION AUTHOR N.KULAHIN,K.K.RASMUSSEN,O.KRISTENSEN,V.BEREZIN,E.BOCK, AUTHOR 2 P.WALMOD,M.GAJHEDE REVDAT 5 23-FEB-11 2V44 1 OBSLTE REVDAT 4 24-FEB-09 2V44 1 VERSN REVDAT 3 16-SEP-08 2V44 1 REMARK DBREF SEQADV HET REVDAT 3 2 HETNAM FORMUL HELIX SHEET REVDAT 3 3 SSBOND CISPEP SITE SCALE1 REVDAT 3 4 SCALE2 SCALE3 ATOM TER REVDAT 3 5 CONECT REVDAT 2 05-AUG-08 2V44 1 SSBOND REVDAT 1 29-JUL-08 2V44 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 IG1-2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.6 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 19936 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.2080 REMARK 3 FREE R VALUE : 0.2453 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1018 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 2V44 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-07. REMARK 100 THE PDBE ID CODE IS EBI-33032. 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) : 120 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) : 0.9072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.77 REMARK 200 RESOLUTION RANGE LOW (A) : 40.50 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.1 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.3 REMARK 200 R MERGE FOR SHELL (I) : 0.68 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.10 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 (%): 52.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.6 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG-4000, 0.2 M SODIUM REMARK 280 ACETATE 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 67.69367 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 135.38733 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 135.38733 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 67.69367 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 375 REMARK 375 SPECIAL POSITION REMARK 375 HOH A2064 LIES ON A SPECIAL POSITION. 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 GLU A 153 REMARK 465 GLU A 154 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 SER A 140 169.46 177.28 REMARK 500 ASN A 169 -1.01 72.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 151 ASN A 152 145.87 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1188 REMARK 900 REMARK 900 RELATED ENTRIES 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 999 REMARK 999 SEQUENCE REMARK 999 3 AMINO ACID DIFFERENCE BETWEEN UNIPROT SEQUENCE AND REMARK 999 SEQUENCE OF THE CRYSTALLIZED PROTEIN DBREF 2V44 A 19 207 UNP O15394 NCAM2_HUMAN 19 207 SEQADV 2V44 GLU A 49 UNP O15394 ARG 49 CONFLICT SEQADV 2V44 GLU A 72 UNP O15394 GLY 72 CONFLICT SEQADV 2V44 PHE A 163 UNP O15394 LEU 163 CONFLICT 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 HET GOL A1188 6 HETNAM GOL GLYCEROL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *164(H2 O1) 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 ARG A 118 0 SHEET 2 AC 2 ARG A 137 SER A 139 -1 O ARG A 137 N ARG A 118 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 HIS A 151 -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 2.04 SSBOND 3 CYS A 136 CYS A 186 1555 1555 2.04 CISPEP 1 SER A 122 PRO A 123 0 1.16 CISPEP 2 SER A 141 PRO A 142 0 -1.46 SITE 1 AC1 6 PRO A 144 ALA A 145 VAL A 146 ASN A 169 SITE 2 AC1 6 HOH A2080 HOH A2163 CRYST1 41.970 41.970 203.081 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 0.023827 0.013756 0.000000 0.00000 SCALE2 0.000000 0.027512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004924 0.00000