HEADER RETINOL-BINDING PROTEIN 18-DEC-14 4UET TITLE DIVERSITY IN THE STRUCTURES AND LIGAND BINDING SITES AMONG THE FATTY TITLE 2 ACID AND RETINOL BINDING PROTEINS OF NEMATODES REVEALED BY NA-FAR-1 TITLE 3 FROM NECATOR AMERICANUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEMATODE FATTY ACID RETINOID BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 21-175; COMPND 5 SYNONYM: NA-FAR-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NECATOR AMERICANUS; SOURCE 3 ORGANISM_TAXID: 51031; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS RETINOL-BINDING PROTEIN, FATTY ACID BINDING, RETINOL BINDING, ALL- KEYWDS 2 ALPHA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.F.REY-BURUSCO,M.IBANEZ SHIMABUKURO,K.GRIFFITHS,A.COOPER, AUTHOR 2 M.W.KENNEDY,B.CORSICO,B.O.SMITH,K.GRIFFITHS REVDAT 3 23-OCT-19 4UET 1 REMARK ATOM REVDAT 2 28-OCT-15 4UET 1 JRNL REVDAT 1 16-SEP-15 4UET 0 JRNL AUTH M.F.REY BURUSCO,M.IBANEZ SHIMABUKURO,M.GABRIELSEN, JRNL AUTH 2 G.R.FRANCHINI,A.J.ROE,K.GRIFFITHS,B.ZHAN,A.COOPER, JRNL AUTH 3 M.W.KENNEDY,B.CORSICO,B.O.SMITH JRNL TITL DIVERSITY IN THE STRUCTURES AND LIGAND BINDING SITES OF JRNL TITL 2 NEMATODE FATTY ACID AND RETINOL BINDING PROTEINS REVEALED BY JRNL TITL 3 NA-FAR-1 FROM NECATOR AMERICANUS. JRNL REF BIOCHEM.J. V. 471 403 2015 JRNL REFN ISSN 0264-6021 JRNL PMID 26318523 JRNL DOI 10.1042/BJ20150068 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.F.REY-BURUSCO,M.IBANEZ-SHIMABUKURO,A.COOPER,M.W.KENNEDY, REMARK 1 AUTH 2 B.CORSICO,B.O.SMITH REMARK 1 TITL 1H, 13C AND 15N CHEMICAL SHIFT ASSIGNMENTS OF NA-FAR-1, A REMARK 1 TITL 2 HELIX-RICH FATTY ACID AND RETINOL BINDING PROTEIN OF THE REMARK 1 TITL 3 PARASITIC NEMATODE NECATOR AMERICANUS. REMARK 1 REF BIOMOL.NMR ASSIGNMENTS V. 8 19 2014 REMARK 1 REFN ISSN 1874-2718 REMARK 1 PMID 23179061 REMARK 1 DOI 10.1007/S12104-012-9444-4 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3/CNS 2.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 4UET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062625. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 311.0 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.07 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : C HSQC3; C NOESY; CBCACONH3; REMARK 210 CBHD; CBHE; COSY; HCCHTOCSY3 1; REMARK 210 HNCACB3; HNCACO3; HNCO3; HSQC3 5; REMARK 210 HCCCONH3; N NOESY; HCCH TOCSY3; REMARK 210 P_A_CAHA_D; P_A_CAHA_U; P_A_NH_D; REMARK 210 P_A_NH_U REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3.1, CCPNMR ANALYSIS 2.1, REMARK 210 DANGLE 1.1, CCPNMR ANALYSIS 2.4, REMARK 210 CCPNMR ANALYSIS 2.0 REMARK 210 METHOD USED : NONE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BEST RESTRAINT ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: INPUT 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 HZ2 LYS A 53 OE2 GLU A 64 1.57 REMARK 500 OD2 ASP A 12 HZ1 LYS A 147 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 12 PHE A 1 CE1 PHE A 1 CZ 0.213 REMARK 500 12 PHE A 1 CZ PHE A 1 CE2 -0.200 REMARK 500 19 TYR A 100 CZ TYR A 100 CE2 -0.083 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 HIS A -6 126.91 72.01 REMARK 500 1 HIS A -5 -35.96 -152.77 REMARK 500 1 ALA A 39 -74.93 -76.64 REMARK 500 1 GLU A 86 39.46 -84.26 REMARK 500 1 LYS A 87 -43.27 -149.51 REMARK 500 1 ASN A 103 56.88 -93.60 REMARK 500 1 GLU A 154 84.21 58.09 REMARK 500 2 SER A -4 80.37 -158.57 REMARK 500 2 MET A 0 -166.83 -78.03 REMARK 500 2 ASP A 27 -47.83 -176.02 REMARK 500 2 ALA A 39 -79.16 -69.56 REMARK 500 2 LYS A 141 -73.69 -50.25 REMARK 500 2 GLU A 154 67.20 -176.79 REMARK 500 3 HIS A -6 166.15 68.26 REMARK 500 3 SER A -4 70.13 63.83 REMARK 500 3 LYS A 2 -83.15 -120.86 REMARK 500 3 TYR A 3 -42.74 167.25 REMARK 500 3 ALA A 39 -78.90 -101.97 REMARK 500 3 GLU A 154 170.88 66.39 REMARK 500 4 SER A -11 -60.99 68.90 REMARK 500 4 HIS A -9 74.80 -114.67 REMARK 500 4 HIS A -8 -158.51 -134.45 REMARK 500 4 HIS A -5 77.61 57.84 REMARK 500 4 SER A -3 35.26 -90.49 REMARK 500 4 SER A 26 55.27 -159.23 REMARK 500 4 ASP A 27 143.06 71.98 REMARK 500 4 LYS A 141 -75.71 -50.50 REMARK 500 4 GLU A 154 9.46 -159.05 REMARK 500 5 PRO A 7 115.36 -37.81 REMARK 500 5 SER A 26 -64.22 -131.58 REMARK 500 5 ASP A 27 -90.49 -135.76 REMARK 500 5 LYS A 141 -75.09 -58.41 REMARK 500 6 SER A -11 60.88 -102.84 REMARK 500 6 HIS A -8 55.30 -147.39 REMARK 500 6 SER A -3 41.47 -140.99 REMARK 500 6 ALA A 39 -77.98 -102.80 REMARK 500 6 LYS A 141 -71.67 -49.63 REMARK 500 6 GLU A 154 170.58 68.17 REMARK 500 7 HIS A -1 45.34 -84.46 REMARK 500 7 MET A 0 119.01 -160.94 REMARK 500 7 GLU A 17 42.62 -77.21 REMARK 500 7 ALA A 18 -38.65 -156.79 REMARK 500 7 SER A 26 -73.59 -112.39 REMARK 500 7 ASP A 27 -86.31 -140.03 REMARK 500 7 ALA A 39 -77.18 -103.10 REMARK 500 7 GLU A 46 -43.54 -156.72 REMARK 500 7 GLU A 154 175.36 71.66 REMARK 500 8 SER A -11 47.78 -85.09 REMARK 500 8 HIS A -10 23.49 -160.47 REMARK 500 8 HIS A -9 63.59 -118.99 REMARK 500 REMARK 500 THIS ENTRY HAS 145 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 PHE A 37 0.06 SIDE CHAIN REMARK 500 9 PHE A 37 0.07 SIDE CHAIN REMARK 500 12 PHE A 37 0.08 SIDE CHAIN REMARK 500 13 PHE A 37 0.06 SIDE CHAIN REMARK 500 15 PHE A 37 0.07 SIDE CHAIN REMARK 500 19 PHE A 37 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18637 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 INCLUDES N-TERMINAL NON-CLEAVABLE HIS-TAG AND CLONING REMARK 999 ARTEFACT. DBREF 4UET A 1 155 UNP W2SRJ3 W2SRJ3_NECAM 21 175 SEQADV 4UET MET A -14 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET GLY A -13 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET SER A -12 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET SER A -11 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -10 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -9 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -8 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -7 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -6 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -5 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET SER A -4 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET SER A -3 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET GLY A -2 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET HIS A -1 UNP W2SRJ3 EXPRESSION TAG SEQADV 4UET MET A 0 UNP W2SRJ3 EXPRESSION TAG SEQRES 1 A 170 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 170 HIS MET PHE LYS TYR GLU ASP ILE PRO ALA ASP TYR ARG SEQRES 3 A 170 ASP LEU MET PRO PRO GLU ALA ARG ASP PHE LEU GLN ASN SEQRES 4 A 170 LEU SER ASP GLY ASP LYS THR VAL LEU LYS GLU VAL PHE SEQRES 5 A 170 LYS ALA GLY PRO TYR LYS ASN THR GLU GLU SER ILE ALA SEQRES 6 A 170 ALA LEU LYS LYS LYS SER PRO GLU LEU GLY ALA LYS VAL SEQRES 7 A 170 GLU LYS LEU HIS ALA MET VAL LYS SER LYS ILE ALA ALA SEQRES 8 A 170 LEU GLY PRO GLU ALA LYS GLY PHE ALA GLU LYS SER ILE SEQRES 9 A 170 GLU ILE ALA ARG GLY ILE LYS ALA ARG TYR TYR THR GLY SEQRES 10 A 170 ASN GLU PRO THR LYS ASP ASP LEU LYS ALA SER VAL LYS SEQRES 11 A 170 GLU VAL LEU LYS LEU TYR LYS ALA MET SER ASP ALA GLY SEQRES 12 A 170 LYS ALA ASP PHE GLY LYS GLN PHE PRO PHE LEU ALA LYS SEQRES 13 A 170 VAL PHE GLU SER GLY LYS ALA ALA LYS PHE ALA GLY GLU SEQRES 14 A 170 ASN HELIX 1 2 LYS A 2 ILE A 6 5 5 HELIX 2 3 PRO A 7 ASP A 12 1 6 HELIX 3 4 PRO A 16 LEU A 25 1 10 HELIX 4 5 SER A 26 GLY A 40 1 15 HELIX 5 6 ASN A 44 SER A 56 1 13 HELIX 6 7 SER A 56 ALA A 76 1 21 HELIX 7 8 GLY A 78 ARG A 98 1 21 HELIX 8 9 THR A 106 LYS A 122 1 17 HELIX 9 10 SER A 125 PHE A 136 1 12 HELIX 10 11 PHE A 136 SER A 145 1 10 HELIX 11 12 ALA A 148 GLY A 153 1 6 CISPEP 1 GLY A 40 PRO A 41 1 -7.73 CISPEP 2 GLY A 40 PRO A 41 2 -8.55 CISPEP 3 GLY A 40 PRO A 41 3 -9.92 CISPEP 4 GLY A 40 PRO A 41 4 -1.12 CISPEP 5 GLY A 40 PRO A 41 5 0.91 CISPEP 6 GLY A 40 PRO A 41 6 -8.23 CISPEP 7 GLY A 40 PRO A 41 7 -8.55 CISPEP 8 GLY A 40 PRO A 41 8 0.69 CISPEP 9 GLY A 40 PRO A 41 9 7.77 CISPEP 10 GLY A 40 PRO A 41 10 -7.97 CISPEP 11 GLY A 40 PRO A 41 11 1.38 CISPEP 12 GLY A 40 PRO A 41 12 -2.43 CISPEP 13 GLY A 40 PRO A 41 13 -0.58 CISPEP 14 GLY A 40 PRO A 41 14 -9.50 CISPEP 15 GLY A 40 PRO A 41 15 -7.70 CISPEP 16 GLY A 40 PRO A 41 16 -7.76 CISPEP 17 GLY A 40 PRO A 41 17 -12.44 CISPEP 18 GLY A 40 PRO A 41 18 -2.63 CISPEP 19 GLY A 40 PRO A 41 19 -6.99 CISPEP 20 GLY A 40 PRO A 41 20 -9.36 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