HEADER PROTEIN BINDING 19-FEB-13 2M5A TITLE PROTEIN A BINDING BY AN ENGINEERED AFFIBODY MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IGG-BINDING PROTEIN A, STAPHYLOCOCCAL PROTEIN A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ZPA963; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: SPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 OTHER_DETAILS: IN-HOUSE STANDARD EXPRESSION VECTOR WITH T7 PROMOTER; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 OTHER_DETAILS: IN-HOUSE STANDARD EXPRESSION VECTOR WITH T7 PROMOTER KEYWDS BINDING PROTEIN, PROTEIN ENGINEERING, PROTEIN A, Z DOMAIN, AFFIBODY KEYWDS 2 MOLECULE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.HARD REVDAT 3 01-MAY-24 2M5A 1 SEQADV REVDAT 2 16-OCT-13 2M5A 1 JRNL REVDAT 1 21-AUG-13 2M5A 0 JRNL AUTH M.LINDBORG,A.DUBNOVITSKY,K.OLESEN,T.BJORKMAN,L.ABRAHMSEN, JRNL AUTH 2 J.FELDWISCH,T.HARD JRNL TITL HIGH-AFFINITY BINDING TO STAPHYLOCOCCAL PROTEIN A BY AN JRNL TITL 2 ENGINEERED DIMERIC AFFIBODY MOLECULE. JRNL REF PROTEIN ENG.DES.SEL. V. 26 635 2013 JRNL REFN ISSN 1741-0126 JRNL PMID 23924760 JRNL DOI 10.1093/PROTEIN/GZT038 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR, ARIA REMARK 3 AUTHORS : VARIAN (VNMR), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103226. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 0.095 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 TO 1 MM [U-99% 13C; U-99% REMARK 210 15N] Z DOMAIN, 25% MOLAR EXCESS REMARK 210 MM ZPA963, 93% H2O/7% D2O; 0.5 REMARK 210 TO 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 ZPA963, 25 5 MOLAR EXCESS MM Z REMARK 210 DOMAIN, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCACB; 3D HN(COCA)CB; 3D 1H- REMARK 210 15N TOCSY; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC; 2D (HB)CB(CGCDCE) REMARK 210 HE; 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D F1(13C,15N)- REMARK 210 FILTERED, F2(13C)-EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CCPNMR, DANGLE, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 PHE A 5 74.39 65.73 REMARK 500 1 ASN A 6 -173.75 -62.96 REMARK 500 1 PRO A 57 -164.63 -71.36 REMARK 500 1 ASN B 106 -67.91 -124.58 REMARK 500 1 LYS B 107 -60.12 -135.27 REMARK 500 1 PRO B 138 -5.16 -58.68 REMARK 500 2 ASN A 6 -169.60 -61.75 REMARK 500 2 PRO A 57 -156.31 -90.66 REMARK 500 2 ASN B 106 -79.22 -114.01 REMARK 500 2 LYS B 107 -60.28 -125.09 REMARK 500 2 ASP B 137 70.55 -151.18 REMARK 500 3 ASN A 3 101.83 -164.79 REMARK 500 3 LYS A 4 -3.41 -59.62 REMARK 500 3 PHE A 5 82.48 67.88 REMARK 500 3 ASN A 6 -173.57 -69.83 REMARK 500 3 PRO A 57 -166.46 -72.59 REMARK 500 3 LYS B 104 -75.44 -95.20 REMARK 500 3 ASN B 106 -69.26 -139.05 REMARK 500 3 LYS B 107 -62.68 -142.06 REMARK 500 3 ASN B 123 -169.60 -77.09 REMARK 500 3 ASP B 137 76.94 -166.23 REMARK 500 3 PRO B 138 -8.46 -58.85 REMARK 500 4 PHE A 5 80.24 67.69 REMARK 500 4 ASN A 6 -169.43 -74.80 REMARK 500 4 ASN B 106 -68.14 -140.60 REMARK 500 4 LYS B 107 -65.32 -137.98 REMARK 500 4 LEU B 119 103.10 -44.49 REMARK 500 4 ASP B 137 71.73 -154.46 REMARK 500 5 ASP A 2 -164.73 57.85 REMARK 500 5 ASN A 3 15.87 59.07 REMARK 500 5 ASN A 6 -170.68 -66.37 REMARK 500 5 LYS B 104 -72.32 -76.17 REMARK 500 5 ASN B 106 -72.74 -137.42 REMARK 500 5 LYS B 107 -68.14 -121.47 REMARK 500 5 ASP B 137 75.60 -161.63 REMARK 500 5 PRO B 138 1.50 -59.74 REMARK 500 5 PRO B 157 -73.52 -55.46 REMARK 500 6 ASP A 2 45.94 -95.57 REMARK 500 6 PHE A 5 74.62 65.99 REMARK 500 6 ASN A 6 -171.26 -69.44 REMARK 500 6 PRO A 57 -165.01 -76.69 REMARK 500 6 ASN B 106 -71.74 -47.36 REMARK 500 6 LYS B 107 -58.76 -137.69 REMARK 500 6 GLU B 108 -37.21 -38.17 REMARK 500 6 PRO B 138 -2.25 -58.98 REMARK 500 6 PRO B 157 -75.47 -73.56 REMARK 500 7 ASN A 3 -73.61 -140.90 REMARK 500 7 PHE A 5 48.64 -91.49 REMARK 500 7 ASN A 6 -170.42 -61.98 REMARK 500 7 PRO A 57 -162.98 -68.84 REMARK 500 REMARK 500 THIS ENTRY HAS 164 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H0T RELATED DB: PDB REMARK 900 RELATED ID: 19043 RELATED DB: BMRB DBREF 2M5A A 2 58 UNP P38507 SPA_STAAU 213 269 DBREF 2M5A B 101 158 PDB 2M5A 2M5A 101 158 SEQADV 2M5A VAL A 1 UNP P38507 EXPRESSION TAG SEQADV 2M5A ALA A 29 UNP P38507 GLY 240 CONFLICT SEQRES 1 A 58 VAL ASP ASN LYS PHE ASN LYS GLU GLN GLN ASN ALA PHE SEQRES 2 A 58 TYR GLU ILE LEU HIS LEU PRO ASN LEU ASN GLU GLU GLN SEQRES 3 A 58 ARG ASN ALA PHE ILE GLN SER LEU LYS ASP ASP PRO SER SEQRES 4 A 58 GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN SEQRES 5 A 58 ASP ALA GLN ALA PRO LYS SEQRES 1 B 58 VAL ASP ASN LYS PHE ASN LYS GLU THR GLN GLU ALA SER SEQRES 2 B 58 TRP GLU ILE PHE THR LEU PRO ASN LEU ASN GLY ARG GLN SEQRES 3 B 58 VAL ALA ALA PHE ILE SER SER LEU LEU ASP ASP PRO SER SEQRES 4 B 58 GLN SER ALA ASN LEU LEU ALA GLU ALA LYS LYS LEU ASN SEQRES 5 B 58 ASP ALA GLN ALA PRO LYS HELIX 1 1 ASN A 6 LEU A 19 1 14 HELIX 2 2 ASN A 23 ASP A 37 1 15 HELIX 3 3 PRO A 38 SER A 41 5 4 HELIX 4 4 ALA A 42 ASP A 53 1 12 HELIX 5 5 LYS B 107 THR B 118 1 12 HELIX 6 6 ASN B 123 ASP B 137 1 15 HELIX 7 7 GLN B 140 ALA B 156 1 17 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