HEADER PROTEIN BINDING 17-AUG-20 7A2D TITLE STRUCTURE-FUNCTION ANALYSES OF DUAL-BON DOMAIN PROTEIN DOLP IDENTIFIES TITLE 2 PHOSPHOLIPID BINDING AS A NEW MECHANISM FOR PROTEIN LOCALISATION TO TITLE 3 THE CELL DIVISION SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YRAP; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 201-91; COMPND 5 SYNONYM: DOLP; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YRAP, B3150, JW3119, WCM_00535; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET26B KEYWDS OUTER MEMBRANE BIOGENESIS, GRAM NEGATIVE, LIPOPROTEIN, YRAP, LIPID KEYWDS 2 BIOGENESIS, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.A.BRYANT,F.C.MORRIS,T.J.KNOWLES,R.MADERBOCUS,E.HEINZ,G.BOELTER, AUTHOR 2 D.ALODAINI,A.COLYER,P.J.WOTHERSPOON,K.A.STAUNTON,M.JEEVES, AUTHOR 3 D.F.BROWNING,Y.R.SEVASTSYANOVICH,T.J.WELLS,A.E.ROSSITER,V.N.BAVRO, AUTHOR 4 P.SRIDHAR,D.G.WARD,Z.S.CHONG,E.C.A.GOODALL,C.ICKE,A.TEO,S.S.CHNG, AUTHOR 5 D.I.ROPER,T.LITHGOW,A.F.CUNNINGHAM,M.BANZHAF,M.OVERDUIN, AUTHOR 6 I.R.HENDERSON REVDAT 5 15-MAY-24 7A2D 1 REMARK REVDAT 4 10-FEB-21 7A2D 1 JRNL REVDAT 3 27-JAN-21 7A2D 1 JRNL REVDAT 2 20-JAN-21 7A2D 1 COMPND SOURCE AUTHOR DBREF REVDAT 2 2 1 SEQADV REVDAT 1 30-DEC-20 7A2D 0 JRNL AUTH J.A.BRYANT,F.C.MORRIS,T.J.KNOWLES,R.MADERBOCUS,E.HEINZ, JRNL AUTH 2 G.BOELTER,D.ALODAINI,A.COLYER,P.J.WOTHERSPOON,K.A.STAUNTON, JRNL AUTH 3 M.JEEVES,D.F.BROWNING,Y.R.SEVASTSYANOVICH,T.J.WELLS, JRNL AUTH 4 A.E.ROSSITER,V.N.BAVRO,P.SRIDHAR,D.G.WARD,Z.S.CHONG, JRNL AUTH 5 E.C.GOODALL,C.ICKE,A.C.TEO,S.S.CHNG,D.I.ROPER,T.LITHGOW, JRNL AUTH 6 A.F.CUNNINGHAM,M.BANZHAF,M.OVERDUIN,I.R.HENDERSON JRNL TITL STRUCTURE OF DUAL BON-DOMAIN PROTEIN DOLP IDENTIFIES JRNL TITL 2 PHOSPHOLIPID BINDING AS A NEW MECHANISM FOR PROTEIN JRNL TITL 3 LOCALISATION. JRNL REF ELIFE V. 9 2020 JRNL REFN ESSN 2050-084X JRNL PMID 33315009 JRNL DOI 10.7554/ELIFE.62614 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, PROCHECK / PROCHECK-NMR, CYANA 2.1 REMARK 3 AUTHORS : LINGE (ARIA), LASKOWSKI, MACARTHUR, SMITH, JONES, REMARK 3 HUTCHINSON, MORRIS, MOSS AND THORNTON (PROCHECK / REMARK 3 PROCHECK-NMR), LASKOWSKI AND MACARTHUR REMARK 3 (PROCHECKNMR) (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7A2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1292109280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT BAR REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-13C; U-15N] DOLP, 50 REMARK 210 MM NA SODIUM PHOSPHATE, 0.02 % W/ REMARK 210 V NA NAN3, 50 MM NA SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HCCH-TOCSY; REMARK 210 3D HN(CO)CA; 3D HNCA; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D HNCO; 3D HN(CA) REMARK 210 CO; 3D 1H-13C NOESY-HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY-HSQC REMARK 210 AROMATIC; 3D 1H-15N NOESY-HSQC; REMARK 210 H(C)CONH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, CYANA, NMRPIPE, REMARK 210 TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THE STRUCTURE WAS CALCULATED USING TRADITIONAL NOE AND REMARK 210 DEHEDRAL ANGLE RESTRAINTS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 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 HG1 THR A 163 OE1 GLU A 166 1.59 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 ALA A 23 73.99 -119.64 REMARK 500 1 ASP A 102 78.70 174.99 REMARK 500 1 ASN A 153 -21.52 70.55 REMARK 500 1 LYS A 191 61.70 24.76 REMARK 500 1 LEU A 194 87.08 48.15 REMARK 500 2 ALA A 23 74.94 -101.68 REMARK 500 2 VAL A 24 49.84 -95.86 REMARK 500 2 ASP A 102 55.12 -177.24 REMARK 500 2 ASN A 153 82.21 -53.08 REMARK 500 2 LYS A 191 90.03 -39.47 REMARK 500 3 ALA A 29 -154.95 -107.44 REMARK 500 3 LYS A 33 99.85 -165.76 REMARK 500 3 ASP A 102 75.73 176.53 REMARK 500 3 PRO A 116 -159.24 -72.77 REMARK 500 3 ASN A 146 -45.71 -156.91 REMARK 500 3 ASN A 153 96.47 -56.25 REMARK 500 3 LYS A 191 -22.45 56.30 REMARK 500 4 LYS A 33 -166.52 -119.36 REMARK 500 4 THR A 36 101.01 71.34 REMARK 500 4 ASP A 102 61.59 -176.45 REMARK 500 4 SER A 145 62.29 -103.64 REMARK 500 4 ASN A 146 23.98 -146.95 REMARK 500 4 ASN A 153 52.69 29.00 REMARK 500 4 LYS A 191 98.34 -38.71 REMARK 500 5 VAL A 24 49.69 -80.13 REMARK 500 5 ALA A 35 44.53 -91.15 REMARK 500 5 PRO A 38 30.71 -75.18 REMARK 500 5 VAL A 41 82.40 71.84 REMARK 500 5 ASP A 102 50.29 -179.35 REMARK 500 5 LYS A 191 -80.61 54.82 REMARK 500 5 LEU A 194 -102.92 -135.33 REMARK 500 5 GLU A 195 -34.34 179.99 REMARK 500 6 ALA A 23 -78.22 -127.30 REMARK 500 6 VAL A 25 -165.75 -121.45 REMARK 500 6 ALA A 28 146.54 76.97 REMARK 500 6 VAL A 30 42.33 -96.39 REMARK 500 6 ARG A 39 67.60 37.86 REMARK 500 6 GLN A 76 -58.84 73.83 REMARK 500 6 ASP A 102 89.35 175.20 REMARK 500 6 PRO A 116 -136.46 -71.40 REMARK 500 6 ALA A 186 72.45 -114.01 REMARK 500 6 LYS A 191 76.12 16.53 REMARK 500 7 VAL A 30 -53.81 -129.20 REMARK 500 7 ASP A 102 47.03 -173.53 REMARK 500 7 ARG A 112 43.35 -71.64 REMARK 500 7 ASN A 146 -69.60 -124.73 REMARK 500 7 LYS A 191 84.93 -10.05 REMARK 500 8 VAL A 30 -156.60 -129.53 REMARK 500 8 ALA A 34 -60.27 73.27 REMARK 500 8 THR A 36 63.77 60.08 REMARK 500 REMARK 500 THIS ENTRY HAS 142 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19760 RELATED DB: BMRB REMARK 900 RELATED ID: 34552 RELATED DB: BMRB REMARK 900 STRUCTURE-FUNCTION ANALYSES OF DUAL-BON DOMAIN PROTEIN DOLP REMARK 900 IDENTIFIES PHOSPHOLIPID BINDING AS A NEW MECHANISM FOR PROTEIN REMARK 900 LOCALISATION TO THE CELL DIVISION SITE DBREF 7A2D A 20 191 UNP P64596 YRAP_ECOLI 20 191 SEQADV 7A2D ILE A 20 UNP P64596 VAL 20 CONFLICT SEQADV 7A2D GLY A 192 UNP P64596 EXPRESSION TAG SEQADV 7A2D GLY A 193 UNP P64596 EXPRESSION TAG SEQADV 7A2D LEU A 194 UNP P64596 EXPRESSION TAG SEQADV 7A2D GLU A 195 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 196 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 197 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 198 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 199 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 200 UNP P64596 EXPRESSION TAG SEQADV 7A2D HIS A 201 UNP P64596 EXPRESSION TAG SEQRES 1 A 182 ILE ALA ALA ALA VAL VAL GLY THR ALA ALA VAL GLY THR SEQRES 2 A 182 LYS ALA ALA THR ASP PRO ARG SER VAL GLY THR GLN VAL SEQRES 3 A 182 ASP ASP GLY THR LEU GLU VAL ARG VAL ASN SER ALA LEU SEQRES 4 A 182 SER LYS ASP GLU GLN ILE LYS LYS GLU ALA ARG ILE ASN SEQRES 5 A 182 VAL THR ALA TYR GLN GLY LYS VAL LEU LEU VAL GLY GLN SEQRES 6 A 182 SER PRO ASN ALA GLU LEU SER ALA ARG ALA LYS GLN ILE SEQRES 7 A 182 ALA MET GLY VAL ASP GLY ALA ASN GLU VAL TYR ASN GLU SEQRES 8 A 182 ILE ARG GLN GLY GLN PRO ILE GLY LEU GLY GLU ALA SER SEQRES 9 A 182 ASN ASP THR TRP ILE THR THR LYS VAL ARG SER GLN LEU SEQRES 10 A 182 LEU THR SER ASP LEU VAL LYS SER SER ASN VAL LYS VAL SEQRES 11 A 182 THR THR GLU ASN GLY GLU VAL PHE LEU MET GLY LEU VAL SEQRES 12 A 182 THR GLU ARG GLU ALA LYS ALA ALA ALA ASP ILE ALA SER SEQRES 13 A 182 ARG VAL SER GLY VAL LYS ARG VAL THR THR ALA PHE THR SEQRES 14 A 182 PHE ILE LYS GLY GLY LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASP A 46 ASP A 61 1 16 HELIX 2 AA2 ASN A 87 GLY A 100 1 14 HELIX 3 AA3 GLY A 118 THR A 138 1 21 HELIX 4 AA4 THR A 163 VAL A 177 1 15 SHEET 1 AA1 3 ARG A 69 TYR A 75 0 SHEET 2 AA1 3 LYS A 78 GLN A 84 -1 O LEU A 80 N THR A 73 SHEET 3 AA1 3 VAL A 107 ILE A 111 1 O TYR A 108 N LEU A 81 SHEET 1 AA2 3 LYS A 148 GLU A 152 0 SHEET 2 AA2 3 GLU A 155 VAL A 162 -1 O PHE A 157 N THR A 150 SHEET 3 AA2 3 ARG A 182 PHE A 189 1 O THR A 188 N VAL A 162 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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