HEADER MEMBRANE PROTEIN 08-MAR-05 1Z2Q TITLE HIGH-RESOLUTION SOLUTION STRUCTURE OF THE LM5-1 FYVE DOMAIN FROM TITLE 2 LEISHMANIA MAJOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LM5-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FYVE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA MAJOR; SOURCE 3 ORGANISM_TAXID: 5664; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: PGEX-6P-3 KEYWDS MEMBRANE PROTEIN, FYVE DOMAIN, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR H.D.T.MERTENS,J.M.CALLAGHAN,M.J.MCCONVILLE,P.R.GOOLEY REVDAT 5 14-JUN-23 1Z2Q 1 REMARK REVDAT 4 26-FEB-20 1Z2Q 1 REMARK REVDAT 3 07-APR-09 1Z2Q 1 JRNL REMARK REVDAT 2 24-FEB-09 1Z2Q 1 VERSN REVDAT 1 19-APR-05 1Z2Q 0 JRNL AUTH H.D.T.MERTENS,J.M.CALLAGHAN,J.D.SWARBRICK,M.J.MCCONVILLE, JRNL AUTH 2 P.R.GOOLEY JRNL TITL A HIGH-RESOLUTION SOLUTION STRUCTURE OF A TRYPANOSOMATID JRNL TITL 2 FYVE DOMAIN. JRNL REF PROTEIN SCI. V. 16 2552 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17905827 JRNL DOI 10.1110/PS.073009807 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, XPLOR-NIH 2.9.1 REMARK 3 AUTHORS : VARIAN INC. (VNMR), REMARK 3 C.D.SCHWIETERS,J.J.KUSZEWSKI,N.TJANDRA,G.M.CLORE REMARK 3 (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES BASED ON 545 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 101 DIHEDRAL ANGLE RESTRAINTS, AND 259 REMARK 3 RESIDUAL DIPOLAR COUPLINGS. REMARK 4 REMARK 4 1Z2Q COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8MM LM5-1 U-15N, 13C; 50MM REMARK 210 SODIUM PHOSPHATE BUFFER, 50MM REMARK 210 KCL, 1MM DTT, 1MM AEBSF, 0.05% REMARK 210 SODIUM AZIDE; 90% H2O, 10% D2O; REMARK 210 0.8MM LM5-1 U-15N,13C; 50MM REMARK 210 SODIUM PHOSPHATE BUFFER, 50MM REMARK 210 KCL, 1MM DTT, 1MM AEBSF,0.05% REMARK 210 SODIUM AZIDE; 100% D2O; 0.8MM REMARK 210 LM5-1 ~10% 13C; 50MM SODIUM REMARK 210 PHOSPHATE BUFFER, 50MM KCL, 1MM REMARK 210 DTT, 1MM AEBSF, 0.05% SODIUM REMARK 210 AZIDE; 100% D2O; 0.8MM LM5-1 U- REMARK 210 15N,13C; 50MM SODIUM PHOSPHATE REMARK 210 BUFFER, 50MM KCL, 1MM DTT, 1MM REMARK 210 AEBSF, 0.05% SODIUM AZIDE; 10MG/ REMARK 210 ML PF1; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 2D_13C- REMARK 210 CT-HSQC; 2D_15N-HSQC-TROSY, 2D_ REMARK 210 HN(A/B-NC-J)-TROSY, 2D_HN(CO-A/B- REMARK 210 C'CA-J)-TROSY, 3D_1H-DEC_HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.2, XEASY 1.3, CYANA REMARK 210 1.0.7 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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 : 21 REMARK 210 REMARK 210 REMARK: 2 X ZN2+ IONS NOT INCLUDED IN CALCULATIONS, LIGATING REMARK 210 CYSTEINES TREATED AS PROTONATED SULFHYDRYL GROUPS DURING REMARK 210 SIMULATED ANNEALING. 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 O ALA A 56 H GLU A 67 1.58 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 21 74.37 -114.11 REMARK 500 1 ASN A 42 -70.27 -100.69 REMARK 500 2 ALA A 21 71.11 -111.37 REMARK 500 2 ASN A 42 -71.54 -101.65 REMARK 500 3 ALA A 21 68.18 -113.39 REMARK 500 3 ASN A 42 -72.06 -100.90 REMARK 500 4 ALA A 21 70.58 -111.47 REMARK 500 4 ASN A 42 -70.00 -102.88 REMARK 500 5 ALA A 21 72.12 -111.41 REMARK 500 5 ASN A 42 -70.26 -100.71 REMARK 500 5 CYS A 70 -168.41 -75.44 REMARK 500 6 ALA A 21 74.44 -110.96 REMARK 500 6 ASN A 42 -72.21 -101.70 REMARK 500 7 SER A 11 39.80 159.46 REMARK 500 7 ALA A 21 72.62 -116.49 REMARK 500 7 ASN A 42 -70.33 -101.67 REMARK 500 8 ALA A 21 74.53 -112.92 REMARK 500 8 ASN A 42 -71.71 -101.46 REMARK 500 9 ALA A 21 78.07 -112.89 REMARK 500 9 ASN A 42 -69.50 -100.70 REMARK 500 10 ALA A 21 77.54 -111.39 REMARK 500 10 ASN A 42 -71.38 -101.21 REMARK 500 11 ALA A 21 72.76 -116.49 REMARK 500 11 ASN A 42 -70.33 -101.74 REMARK 500 12 ALA A 21 75.71 -112.56 REMARK 500 12 ASN A 42 -70.04 -100.66 REMARK 500 13 ALA A 21 72.61 -112.43 REMARK 500 13 ASN A 42 -71.37 -101.54 REMARK 500 13 SER A 79 -83.66 -60.54 REMARK 500 14 ALA A 21 77.66 -114.54 REMARK 500 14 ASN A 42 -71.82 -101.28 REMARK 500 15 ALA A 21 73.57 -115.48 REMARK 500 15 ASN A 42 -72.31 -101.72 REMARK 500 16 ALA A 21 73.79 -110.68 REMARK 500 16 ASN A 42 -71.64 -100.66 REMARK 500 17 ALA A 21 74.30 -113.61 REMARK 500 17 ASN A 42 -72.53 -101.08 REMARK 500 18 ALA A 21 74.24 -111.84 REMARK 500 18 ASN A 42 -70.26 -102.90 REMARK 500 19 SER A 11 66.67 178.97 REMARK 500 19 ALA A 21 76.45 -109.91 REMARK 500 19 ASN A 42 -70.66 -101.82 REMARK 500 20 ALA A 21 75.63 -115.30 REMARK 500 20 ASN A 42 -71.49 -100.81 REMARK 500 21 LEU A 3 -53.94 -178.63 REMARK 500 21 GLU A 8 -18.91 -47.64 REMARK 500 21 SER A 11 107.62 -19.07 REMARK 500 21 LYS A 12 93.39 -38.32 REMARK 500 21 ASN A 42 -69.32 -92.97 REMARK 500 21 CYS A 70 -157.18 -100.02 REMARK 500 REMARK 500 THIS ENTRY HAS 52 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6594 RELATED DB: BMRB DBREF 1Z2Q A 1 84 PDB 1Z2Q 1Z2Q 1 84 SEQRES 1 A 84 GLY PRO LEU GLY SER MET GLY GLU LYS GLN SER LYS GLY SEQRES 2 A 84 TYR TRP GLN GLU ASP GLU ASP ALA PRO ALA CYS ASN GLY SEQRES 3 A 84 CYS GLY CYS VAL PHE THR THR THR VAL ARG ARG HIS HIS SEQRES 4 A 84 CYS ARG ASN CYS GLY TYR VAL LEU CYS GLY ASP CYS SER SEQRES 5 A 84 ARG HIS ARG ALA ALA ILE PRO MET ARG GLY ILE THR GLU SEQRES 6 A 84 PRO GLU ARG VAL CYS ASP ALA CYS TYR LEU ALA LEU ARG SEQRES 7 A 84 SER SER ASN MET ALA GLY HELIX 1 1 GLY A 49 ARG A 53 5 5 HELIX 2 2 CYS A 70 SER A 79 1 10 SHEET 1 A 2 HIS A 38 HIS A 39 0 SHEET 2 A 2 VAL A 46 LEU A 47 -1 O LEU A 47 N HIS A 38 SHEET 1 B 2 ARG A 55 ILE A 58 0 SHEET 2 B 2 ILE A 63 ARG A 68 -1 O GLU A 67 N ALA A 56 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