PDB Short entry for 1FK1 HEADER LIPID TRANSPORT 09-AUG-00 1FK1 TITLE STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE LIPID-TRANSFER TITLE 2 PROTEIN COMPLEXES WITH LAURIC ACID REVEALED BY HIGH-RESOLUTION X-RAY TITLE 3 CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SPECIFIC LIPID TRANSFER PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_TAXID: 4577 KEYWDS PROTEIN-LIPID COMPLEX, LIPID TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.W.HAN,J.Y.LEE,H.K.SONG,D.H.SHIN,S.W.SUH REVDAT 4 04-OCT-17 1FK1 1 REMARK REVDAT 3 24-FEB-09 1FK1 1 VERSN REVDAT 2 07-JAN-03 1FK1 1 REMARK REVDAT 1 06-JUN-01 1FK1 0 JRNL AUTH G.W.HAN,J.Y.LEE,H.K.SONG,C.CHANG,K.MIN,J.MOON,D.H.SHIN, JRNL AUTH 2 M.L.KOPKA,M.R.SAWAYA,H.S.YUAN,T.D.KIM,J.CHOE,D.LIM,H.J.MOON, JRNL AUTH 3 S.W.SUH JRNL TITL STRUCTURAL BASIS OF NON-SPECIFIC LIPID BINDING IN MAIZE JRNL TITL 2 LIPID-TRANSFER PROTEIN COMPLEXES REVEALED BY HIGH-RESOLUTION JRNL TITL 3 X-RAY CRYSTALLOGRAPHY. JRNL REF J.MOL.BIOL. V. 308 263 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11327766 JRNL DOI 10.1006/JMBI.2001.4559 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 7638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 474 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 625 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 52 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FK1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROFILE-FITTING PROCEDURE, REMARK 200 MADNESS REMARK 200 DATA SCALING SOFTWARE : PROFILE-FITTING PROCEDURE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8622 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 2.690 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: (PDB CODE:1MZL) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.2M NA FORMATE, 0.2M POTASSIUM REMARK 280 CYANIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 12.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.80000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.84000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.80000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.84000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAO A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MZL RELATED DB: PDB REMARK 900 1MZL CONTAINS PHOSPHOLIPID TRANSFER PROTEIN. REMARK 900 RELATED ID: 1MZM RELATED DB: PDB REMARK 900 1MZM CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH PALMITIC REMARK 900 ACID. REMARK 900 RELATED ID: 1FK0 RELATED DB: PDB REMARK 900 1FK0 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH CAPRIC REMARK 900 ACID. REMARK 900 RELATED ID: 1FK2 RELATED DB: PDB REMARK 900 1FK2 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH MYRISTIC REMARK 900 ACID REMARK 900 RELATED ID: 1FK3 RELATED DB: PDB REMARK 900 1FK3 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH REMARK 900 PALMITOLEIC ACID. REMARK 900 RELATED ID: 1FK4 RELATED DB: PDB REMARK 900 1FK4 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH STEARIC REMARK 900 ACID. REMARK 900 RELATED ID: 1FK5 RELATED DB: PDB REMARK 900 1FK5 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH OLEIC REMARK 900 ACID. REMARK 900 RELATED ID: 1FK6 RELATED DB: PDB REMARK 900 1FK6 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH ALPHA- REMARK 900 LINOLENIC ACID. REMARK 900 RELATED ID: 1FK7 RELATED DB: PDB REMARK 900 1FK7 CONTAINS PHOSPHOLIPID TRANSFER PROTEIN COMPLEXED WITH REMARK 900 RICINOLEIC ACID. DBREF 1FK1 A 1 93 UNP P19656 NLTP_MAIZE 28 120 SEQRES 1 A 93 ALA ILE SER CYS GLY GLN VAL ALA SER ALA ILE ALA PRO SEQRES 2 A 93 CYS ILE SER TYR ALA ARG GLY GLN GLY SER GLY PRO SER SEQRES 3 A 93 ALA GLY CYS CYS SER GLY VAL ARG SER LEU ASN ASN ALA SEQRES 4 A 93 ALA ARG THR THR ALA ASP ARG ARG ALA ALA CYS ASN CYS SEQRES 5 A 93 LEU LYS ASN ALA ALA ALA GLY VAL SER GLY LEU ASN ALA SEQRES 6 A 93 GLY ASN ALA ALA SER ILE PRO SER LYS CYS GLY VAL SER SEQRES 7 A 93 ILE PRO TYR THR ILE SER THR SER THR ASP CYS SER ARG SEQRES 8 A 93 VAL ASN HET DAO A 201 14 HET FMT A 202 3 HET FMT A 205 3 HET FMT A 206 3 HETNAM DAO LAURIC ACID HETNAM FMT FORMIC ACID FORMUL 2 DAO C12 H24 O2 FORMUL 3 FMT 3(C H2 O2) FORMUL 6 HOH *52(H2 O) HELIX 1 1 CYS A 4 ALA A 18 1 15 HELIX 2 2 ALA A 27 ALA A 39 1 13 HELIX 3 3 THR A 43 ALA A 58 1 16 HELIX 4 4 ALA A 65 LYS A 74 1 10 SSBOND 1 CYS A 4 CYS A 52 1555 1555 2.16 SSBOND 2 CYS A 14 CYS A 29 1555 1555 2.18 SSBOND 3 CYS A 30 CYS A 75 1555 1555 2.22 SSBOND 4 CYS A 50 CYS A 89 1555 1555 2.21 SITE 1 AC1 5 VAL A 33 ASN A 37 ARG A 46 LEU A 53 SITE 2 AC1 5 ILE A 83 SITE 1 AC2 7 ARG A 47 ALA A 48 ASN A 51 GLY A 62 SITE 2 AC2 7 LEU A 63 HOH A 127 HOH A 155 SITE 1 AC3 4 ALA A 69 PRO A 72 THR A 82 ILE A 83 SITE 1 AC4 6 ASN A 51 LYS A 54 ASN A 64 GLY A 66 SITE 2 AC4 6 THR A 87 CYS A 89 CRYST1 24.820 49.680 69.600 90.00 90.00 90.00 P 21 21 21 4 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 0.040290 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014368 0.00000