PDB Short entry for 1NWV HEADER BIOSYNTHETIC PROTEIN 07-FEB-03 1NWV TITLE SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE COMPONENT OF DECAY TITLE 2 ACCELERATING FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: COMPLEMENT DECAY-ACCELERATING FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CD55 ANTIGEN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DAF OR CR OR CD55; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA KEYWDS CD55, DAF, CCP, COMPLEMENT, BIOSYNTHETIC PROTEIN EXPDTA SOLUTION NMR NUMMDL 42 AUTHOR S.UHRINOVA,F.LIN,G.BALL,K.BROMEK,D.UHRIN,M.E.MEDOF,P.N.BARLOW REVDAT 3 23-FEB-22 1NWV 1 REMARK SEQADV REVDAT 2 24-FEB-09 1NWV 1 VERSN REVDAT 1 22-APR-03 1NWV 0 JRNL AUTH S.UHRINOVA,F.LIN,G.BALL,K.BROMEK,D.UHRIN,M.E.MEDOF, JRNL AUTH 2 P.N.BARLOW JRNL TITL SOLUTION STRUCTURE OF A FUNCTIONALLY ACTIVE FRAGMENT OF JRNL TITL 2 DECAY-ACCELERATING FACTOR JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 4718 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12672958 JRNL DOI 10.1073/PNAS.0730844100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 1997, CNS PARALLHDG5.1 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2440 NOES, 59 RDC REMARK 4 REMARK 4 1NWV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018296. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9 MM PROTEIN -15N,13C; 50MM REMARK 210 SODIUM ACETATE BUFFER; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNCA-J; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1995 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 190 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 42 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING DOUBLE LABELLED SAMPLE 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 HD11 ILE A 172 HA VAL A 177 1.25 REMARK 500 HB3 LEU A 112 H GLN A 113 1.34 REMARK 500 HG12 ILE A 135 H ARG A 136 1.34 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 ARG A 62 -81.13 -123.22 REMARK 500 1 SER A 63 157.83 63.48 REMARK 500 1 VAL A 66 110.37 -36.61 REMARK 500 1 PRO A 67 172.35 -57.66 REMARK 500 1 SER A 72 15.66 -156.73 REMARK 500 1 PRO A 78 36.28 -66.56 REMARK 500 1 ILE A 80 -81.64 -64.24 REMARK 500 1 THR A 81 -32.46 72.05 REMARK 500 1 ASN A 83 -75.10 -117.48 REMARK 500 1 GLU A 102 -179.41 -46.57 REMARK 500 1 PRO A 103 21.76 -54.29 REMARK 500 1 SER A 104 71.14 73.12 REMARK 500 1 LEU A 105 -166.35 -127.14 REMARK 500 1 SER A 106 100.92 -41.45 REMARK 500 1 PRO A 107 56.44 -94.04 REMARK 500 1 LEU A 112 -103.86 -82.80 REMARK 500 1 ASN A 114 50.29 -118.06 REMARK 500 1 LEU A 115 45.93 18.53 REMARK 500 1 TRP A 117 151.88 -42.78 REMARK 500 1 SER A 118 -130.00 -68.57 REMARK 500 1 VAL A 121 -82.61 -103.81 REMARK 500 1 GLU A 122 67.03 -176.64 REMARK 500 1 LYS A 125 -93.04 -148.55 REMARK 500 1 LYS A 126 144.29 178.70 REMARK 500 1 ASN A 131 126.19 64.43 REMARK 500 1 PRO A 132 9.91 -68.81 REMARK 500 1 ILE A 135 -136.14 -67.14 REMARK 500 1 GLN A 139 174.77 172.00 REMARK 500 1 PRO A 143 18.64 -68.89 REMARK 500 1 ALA A 150 -162.67 -110.28 REMARK 500 1 THR A 151 163.81 177.66 REMARK 500 1 PHE A 163 71.39 -117.92 REMARK 500 1 SER A 167 160.16 169.77 REMARK 500 1 SER A 176 -179.86 69.57 REMARK 500 1 VAL A 177 104.07 -51.90 REMARK 500 1 PRO A 182 -153.66 -66.42 REMARK 500 1 PRO A 184 -147.83 -67.88 REMARK 500 2 ARG A 62 -71.04 -100.58 REMARK 500 2 SER A 63 -158.48 -154.79 REMARK 500 2 VAL A 66 117.50 -39.15 REMARK 500 2 PRO A 78 36.96 -69.61 REMARK 500 2 ILE A 80 -84.14 -51.17 REMARK 500 2 THR A 81 -35.69 71.70 REMARK 500 2 ASN A 83 -102.51 -77.28 REMARK 500 2 PRO A 103 64.29 -20.17 REMARK 500 2 SER A 104 94.11 48.08 REMARK 500 2 SER A 106 101.74 -49.18 REMARK 500 2 PRO A 107 57.52 -97.99 REMARK 500 2 LEU A 112 -100.98 -82.65 REMARK 500 2 LEU A 115 47.47 22.13 REMARK 500 REMARK 500 THIS ENTRY HAS 1408 RAMACHANDRAN OUTLIERS. 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 PRO A 78 TYR A 79 2 148.98 REMARK 500 GLU A 102 PRO A 103 2 -145.79 REMARK 500 PRO A 184 GLU A 185 2 146.84 REMARK 500 PRO A 184 GLU A 185 3 141.71 REMARK 500 GLU A 102 PRO A 103 4 128.82 REMARK 500 GLN A 77 PRO A 78 5 146.83 REMARK 500 GLN A 77 PRO A 78 6 147.52 REMARK 500 GLY A 98 TYR A 99 6 -149.01 REMARK 500 GLU A 102 PRO A 103 6 148.69 REMARK 500 GLN A 77 PRO A 78 7 131.74 REMARK 500 LEU A 183 PRO A 184 7 146.32 REMARK 500 LEU A 105 SER A 106 8 133.94 REMARK 500 LEU A 75 LYS A 76 9 137.07 REMARK 500 ASN A 114 LEU A 115 9 -149.05 REMARK 500 GLU A 102 PRO A 103 11 143.28 REMARK 500 PRO A 184 GLU A 185 11 146.68 REMARK 500 GLU A 122 PHE A 123 12 147.28 REMARK 500 PRO A 184 GLU A 185 14 146.15 REMARK 500 LYS A 76 GLN A 77 16 -146.55 REMARK 500 GLN A 77 PRO A 78 16 133.85 REMARK 500 PHE A 123 CYS A 124 16 -133.02 REMARK 500 ARG A 101 GLU A 102 17 147.66 REMARK 500 ALA A 120 VAL A 121 18 -142.45 REMARK 500 ALA A 120 VAL A 121 19 -147.10 REMARK 500 ARG A 101 GLU A 102 20 145.33 REMARK 500 TRP A 117 SER A 118 20 -149.11 REMARK 500 GLN A 77 PRO A 78 21 137.10 REMARK 500 CYS A 111 LEU A 112 21 -143.99 REMARK 500 PHE A 123 CYS A 124 21 -147.66 REMARK 500 PRO A 184 GLU A 185 21 149.76 REMARK 500 CYS A 111 LEU A 112 22 -149.52 REMARK 500 ASN A 114 LEU A 115 22 -149.99 REMARK 500 GLN A 77 PRO A 78 25 143.23 REMARK 500 ARG A 101 GLU A 102 25 142.39 REMARK 500 CYS A 111 LEU A 112 25 -148.12 REMARK 500 GLN A 77 PRO A 78 26 126.56 REMARK 500 CYS A 111 LEU A 112 26 -147.83 REMARK 500 ARG A 101 GLU A 102 27 146.49 REMARK 500 CYS A 111 LEU A 112 27 -147.72 REMARK 500 ARG A 101 GLU A 102 28 149.17 REMARK 500 ALA A 120 VAL A 121 28 -149.24 REMARK 500 ALA A 120 VAL A 121 29 -149.09 REMARK 500 CYS A 111 LEU A 112 30 -147.57 REMARK 500 PHE A 123 CYS A 124 30 -149.23 REMARK 500 ASN A 137 GLY A 138 30 -146.99 REMARK 500 CYS A 111 LEU A 112 31 -145.76 REMARK 500 GLN A 77 PRO A 78 32 138.33 REMARK 500 GLU A 102 PRO A 103 32 147.61 REMARK 500 CYS A 111 LEU A 112 32 -146.87 REMARK 500 GLN A 77 PRO A 78 33 133.04 REMARK 500 REMARK 500 THIS ENTRY HAS 71 NON CIS, NON-TRANS OMEGA OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1NWV A 62 188 UNP P08174 DAF_HUMAN 96 222 SEQADV 1NWV PHE A 61 UNP P08174 CLONING ARTIFACT SEQADV 1NWV HIS A 189 UNP P08174 CLONING ARTIFACT SEQRES 1 A 129 PHE ARG SER CYS GLU VAL PRO THR ARG LEU ASN SER ALA SEQRES 2 A 129 SER LEU LYS GLN PRO TYR ILE THR GLN ASN TYR PHE PRO SEQRES 3 A 129 VAL GLY THR VAL VAL GLU TYR GLU CYS ARG PRO GLY TYR SEQRES 4 A 129 ARG ARG GLU PRO SER LEU SER PRO LYS LEU THR CYS LEU SEQRES 5 A 129 GLN ASN LEU LYS TRP SER THR ALA VAL GLU PHE CYS LYS SEQRES 6 A 129 LYS LYS SER CYS PRO ASN PRO GLY GLU ILE ARG ASN GLY SEQRES 7 A 129 GLN ILE ASP VAL PRO GLY GLY ILE LEU PHE GLY ALA THR SEQRES 8 A 129 ILE SER PHE SER CYS ASN THR GLY TYR LYS LEU PHE GLY SEQRES 9 A 129 SER THR SER SER PHE CYS LEU ILE SER GLY SER SER VAL SEQRES 10 A 129 GLN TRP SER ASP PRO LEU PRO GLU CYS ARG GLU HIS SHEET 1 A 2 ALA A 73 LEU A 75 0 SHEET 2 A 2 TYR A 93 CYS A 95 -1 O GLU A 94 N SER A 74 SHEET 1 B 2 THR A 89 VAL A 91 0 SHEET 2 B 2 LEU A 109 CYS A 111 -1 O LEU A 109 N VAL A 91 SHEET 1 C 4 GLY A 138 ASP A 141 0 SHEET 2 C 4 THR A 151 CYS A 156 -1 O SER A 155 N GLN A 139 SHEET 3 C 4 SER A 168 LEU A 171 -1 O SER A 168 N ILE A 152 SHEET 4 C 4 GLN A 178 TRP A 179 -1 O GLN A 178 N LEU A 171 SHEET 1 D 2 TYR A 160 LEU A 162 0 SHEET 2 D 2 CYS A 186 GLU A 188 -1 O ARG A 187 N LYS A 161 SSBOND 1 CYS A 64 CYS A 111 1555 1555 2.03 SSBOND 2 CYS A 95 CYS A 124 1555 1555 2.03 SSBOND 3 CYS A 129 CYS A 170 1555 1555 2.03 SSBOND 4 CYS A 156 CYS A 186 1555 1555 2.03 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