HEADER METAL BINDING PROTEIN 07-MAY-04 1T6W TITLE RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 TITLE 2 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN XP_346638; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS CALCIUM-BINDING PROTEIN, CD2, DESIGN, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.YANG,A.L.WILKINS,Y.YE,Z.-R.LIU,J.L.URBAUER,A.KEARNEY,P.A.VAN DER AUTHOR 2 MERWE,J.J.YANG REVDAT 4 27-OCT-21 1T6W 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1T6W 1 VERSN REVDAT 2 22-FEB-05 1T6W 1 JRNL REVDAT 1 15-FEB-05 1T6W 0 JRNL AUTH W.YANG,A.L.WILKINS,Y.YE,Z.R.LIU,S.Y.LI,J.L.URBAUER, JRNL AUTH 2 H.W.HELLINGA,A.KEARNEY,P.A.VAN DER MERWE,J.J.YANG JRNL TITL DESIGN OF A CALCIUM-BINDING PROTEIN WITH DESIRED STRUCTURE JRNL TITL 2 IN A CELL ADHESION MOLECULE. JRNL REF J.AM.CHEM.SOC. V. 127 2085 2005 JRNL REFN ISSN 0002-7863 JRNL PMID 15713084 JRNL DOI 10.1021/JA0431307 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1T6W COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022387. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 95% H2O, 5% D2O, PROTEIN 1 MM, REMARK 210 KCL 130 MM, CACL2 10 MM, PIPES REMARK 210 20 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_TOCSY; 15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.1 REMARK 210 METHOD USED : ANNEAL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 ASP A 2 78.94 -100.03 REMARK 500 1 SER A 3 -74.94 -83.03 REMARK 500 1 ILE A 14 136.28 163.29 REMARK 500 1 MET A 23 75.20 -68.78 REMARK 500 1 ALA A 40 113.23 -167.20 REMARK 500 1 LYS A 45 39.40 -82.44 REMARK 500 1 MET A 46 -166.19 41.91 REMARK 500 1 SER A 52 165.97 179.05 REMARK 500 1 ASN A 60 33.25 -97.06 REMARK 500 1 ILE A 88 -67.31 -104.12 REMARK 500 2 ASP A 2 92.21 -62.27 REMARK 500 2 ILE A 14 136.33 160.36 REMARK 500 2 ALA A 40 111.86 -165.76 REMARK 500 2 ARG A 44 -88.98 -51.71 REMARK 500 2 LYS A 45 48.65 -82.59 REMARK 500 2 ASN A 60 31.91 -96.53 REMARK 500 3 ASP A 2 79.96 60.38 REMARK 500 3 ILE A 14 136.19 162.03 REMARK 500 3 ALA A 40 111.31 -166.06 REMARK 500 3 LYS A 45 -47.32 82.48 REMARK 500 3 ASN A 60 32.81 -96.13 REMARK 500 4 ASP A 2 -68.57 68.33 REMARK 500 4 ILE A 14 136.61 161.24 REMARK 500 4 ALA A 40 114.38 -174.73 REMARK 500 4 LYS A 45 46.72 -82.56 REMARK 500 4 MET A 46 -171.86 177.59 REMARK 500 4 LYS A 51 -90.33 -38.88 REMARK 500 4 ASN A 60 31.94 -96.24 REMARK 500 5 ILE A 14 136.02 163.31 REMARK 500 5 ALA A 40 112.17 -167.47 REMARK 500 5 ARG A 44 90.27 -59.83 REMARK 500 5 LYS A 45 -45.56 80.85 REMARK 500 5 ASN A 60 33.33 -96.76 REMARK 500 6 SER A 3 108.05 60.48 REMARK 500 6 ILE A 14 136.00 163.79 REMARK 500 6 ALA A 40 110.17 -166.60 REMARK 500 6 LYS A 45 46.35 -82.19 REMARK 500 6 MET A 46 -172.40 176.19 REMARK 500 6 LEU A 58 165.75 -49.19 REMARK 500 6 ASN A 60 33.11 -96.21 REMARK 500 6 ILE A 88 -69.30 -93.95 REMARK 500 7 ILE A 14 137.24 161.70 REMARK 500 7 ALA A 40 111.57 -166.64 REMARK 500 7 ARG A 44 94.40 -55.76 REMARK 500 7 LYS A 45 -46.98 81.66 REMARK 500 7 ASN A 60 33.12 -96.57 REMARK 500 7 ILE A 88 -70.71 -82.20 REMARK 500 8 ILE A 14 136.65 162.19 REMARK 500 8 ALA A 40 112.55 -162.34 REMARK 500 8 LYS A 45 39.10 -82.24 REMARK 500 REMARK 500 THIS ENTRY HAS 130 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 100 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD2 REMARK 620 2 ASP A 17 OD1 80.8 REMARK 620 3 ASN A 60 OD1 139.3 134.0 REMARK 620 4 ASP A 62 OD1 100.1 79.6 72.8 REMARK 620 5 ASP A 62 OD2 51.8 73.7 110.4 48.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 100 DBREF 1T6W A 1 99 UNP P08921 CD2_RAT 23 121 SEQADV 1T6W ASP A 15 UNP P08921 ASN 37 ENGINEERED MUTATION SEQADV 1T6W ASP A 17 UNP P08921 ASN 39 ENGINEERED MUTATION SEQRES 1 A 99 ARG ASP SER GLY THR VAL TRP GLY ALA LEU GLY HIS GLY SEQRES 2 A 99 ILE ASP LEU ASP ILE PRO ASN PHE GLN MET THR ASP ASP SEQRES 3 A 99 ILE ASP GLU VAL ARG TRP GLU ARG GLY SER THR LEU VAL SEQRES 4 A 99 ALA GLU PHE LYS ARG LYS MET LYS PRO PHE LEU LYS SER SEQRES 5 A 99 GLY ALA PHE GLU ILE LEU ALA ASN GLY ASP LEU LYS ILE SEQRES 6 A 99 LYS ASN LEU THR ARG ASP ASP SER GLY THR TYR ASN VAL SEQRES 7 A 99 THR VAL TYR SER THR ASN GLY THR ARG ILE LEU ASN LYS SEQRES 8 A 99 ALA LEU ASP LEU ARG ILE LEU GLU HET CA A 100 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 THR A 69 SER A 73 5 5 SHEET 1 A 6 THR A 5 ALA A 9 0 SHEET 2 A 6 ARG A 87 LEU A 98 1 O LEU A 98 N GLY A 8 SHEET 3 A 6 GLY A 74 SER A 82 -1 N VAL A 80 O ILE A 88 SHEET 4 A 6 ILE A 27 ARG A 34 -1 N GLU A 33 O ASN A 77 SHEET 5 A 6 THR A 37 LYS A 43 -1 O PHE A 42 N VAL A 30 SHEET 6 A 6 PHE A 49 LEU A 50 -1 O PHE A 49 N GLU A 41 SHEET 1 B 3 ILE A 14 LEU A 16 0 SHEET 2 B 3 LEU A 63 ILE A 65 -1 O ILE A 65 N ILE A 14 SHEET 3 B 3 PHE A 55 ILE A 57 -1 N GLU A 56 O LYS A 64 LINK OD2 ASP A 15 CA CA A 100 1555 1555 2.81 LINK OD1 ASP A 17 CA CA A 100 1555 1555 2.80 LINK OD1 ASN A 60 CA CA A 100 1555 1555 2.81 LINK OD1 ASP A 62 CA CA A 100 1555 1555 2.48 LINK OD2 ASP A 62 CA CA A 100 1555 1555 2.83 SITE 1 AC1 4 ASP A 15 ASP A 17 ASN A 60 ASP A 62 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1