HEADER CELL ADHESION 31-AUG-07 2VAJ TITLE CRYSTAL STRUCTURE OF NCAM2 IG1 (I4122 CELL UNIT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL CELL ADHESION MOLECULE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG1, RESIDUES 21-113; 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: PROCHLOROCOCCUS MARINUS SUBSP. PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 142479; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: KM71H; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PPICZALFAC KEYWDS IMMUNOGLOBULIN DOMAIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.KULAHIN,K.K.RASMUSSEN,O.KRISTENSEN,J.S.KASTRUP,J.-C.NAVARRO- AUTHOR 2 POULSEN,V.BEREZIN,E.BOCK,P.S.WALMOD,M.GAJHEDE REVDAT 5 13-DEC-23 2VAJ 1 REMARK REVDAT 4 17-JAN-18 2VAJ 1 REMARK REVDAT 3 24-FEB-09 2VAJ 1 VERSN REVDAT 2 23-SEP-08 2VAJ 1 AUTHOR JRNL REMARK REVDAT 1 26-AUG-08 2VAJ 0 JRNL AUTH K.K.RASMUSSEN,N.KULAHIN,O.KRISTENSEN,J.C.POULSEN, JRNL AUTH 2 B.W.SIGURSKJOLD,J.S.KASTRUP,V.BEREZIN,E.BOCK,P.S.WALMOD, JRNL AUTH 3 M.GAJHEDE JRNL TITL CRYSTAL STRUCTURE OF THE IG1 DOMAIN OF THE NEURAL CELL JRNL TITL 2 ADHESION MOLECULE NCAM2 DISPLAYS DOMAIN SWAPPING. JRNL REF J.MOL.BIOL. V. 382 1113 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18706912 JRNL DOI 10.1016/J.JMB.2008.07.084 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 3339 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.300 REMARK 3 FREE R VALUE TEST SET COUNT : 145 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 : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 48.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.820 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: 0.3210 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 738 REMARK 3 ANGLE : 1.059 999 REMARK 3 CHIRALITY : 0.068 118 REMARK 3 PLANARITY : 0.004 129 REMARK 3 DIHEDRAL : 20.967 270 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 2VAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 3356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.40 REMARK 200 R MERGE FOR SHELL (I) : 0.10000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.100 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: NCAM IG1 PDB ENTRY 1EPF, CHAIN A REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 23.63950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 23.63950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.36350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.18175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.63950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 147.54525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 147.54525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.63950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.18175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 23.63950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.36350 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 23.63950 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.36350 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 23.63950 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 147.54525 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 49.18175 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 23.63950 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.18175 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 147.54525 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 23.63950 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 23.63950 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 98.36350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 27 56.00 -109.64 REMARK 500 PRO A 36 10.76 -65.00 REMARK 500 THR A 44 -154.91 -113.93 REMARK 500 GLU A 52 62.77 -116.28 REMARK 500 ASN A 62 60.05 39.02 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: 2V44 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG1-2 REMARK 900 RELATED ID: 2VA4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NCAM2 IG34 REMARK 999 REMARK 999 SEQUENCE REMARK 999 2 AMINO ACID DIFFERENCE BETWEEN THE SEQUENCE OF THE REMARK 999 CRYSTALLIZED PROTEIN AND THE DATABASE SEQUENCE DBREF 2VAJ A 1 93 UNP O15394 NCAM2_HUMAN 21 113 SEQADV 2VAJ GLU A 29 UNP O15394 ARG 49 CONFLICT SEQADV 2VAJ GLU A 52 UNP O15394 GLY 72 CONFLICT SEQRES 1 A 93 LEU GLN VAL THR ILE SER LEU SER LYS VAL GLU LEU SER SEQRES 2 A 93 VAL GLY GLU SER LYS PHE PHE THR CYS THR ALA ILE GLY SEQRES 3 A 93 GLU PRO GLU SER ILE ASP TRP TYR ASN PRO GLN GLY GLU SEQRES 4 A 93 LYS ILE ILE SER THR GLN ARG VAL VAL VAL GLN LYS GLU SEQRES 5 A 93 GLY VAL ARG SER ARG LEU THR ILE TYR ASN ALA ASN ILE SEQRES 6 A 93 GLU ASP ALA GLY ILE TYR ARG CYS GLN ALA THR ASP ALA SEQRES 7 A 93 LYS GLY GLN THR GLN GLU ALA THR VAL VAL LEU GLU ILE SEQRES 8 A 93 TYR GLN FORMUL 2 HOH *6(H2 O) HELIX 1 1 ASN A 64 ALA A 68 5 5 SHEET 1 AA 4 LYS A 9 SER A 13 0 SHEET 2 AA 4 THR A 82 TYR A 92 1 O VAL A 88 N VAL A 10 SHEET 3 AA 4 GLY A 69 THR A 76 -1 O GLY A 69 N LEU A 89 SHEET 4 AA 4 SER A 30 TYR A 34 -1 O SER A 30 N THR A 76 SHEET 1 AB 3 LYS A 18 THR A 23 0 SHEET 2 AB 3 ARG A 55 ILE A 60 -1 O SER A 56 N CYS A 22 SHEET 3 AB 3 VAL A 47 GLU A 52 -1 O VAL A 48 N THR A 59 SSBOND 1 CYS A 22 CYS A 73 1555 1555 2.01 CRYST1 47.279 47.279 196.727 90.00 90.00 90.00 I 41 2 2 16 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 0.021151 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005083 0.00000