HEADER LIPID TRANSPORT 09-OCT-97 1RZL TITLE RICE NONSPECIFIC LIPID TRANSFER PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NONSPECIFIC LIPID TRANSFER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FOUR-HELIX BUNDLE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 ORGAN: SEED KEYWDS LIPID TRANSPORT, ALPHA-HELICAL STRUCTURE EXPDTA X-RAY DIFFRACTION AUTHOR J.Y.LEE,K.S.MIN,H.CHA,D.H.SHIN,K.Y.HWANG,S.W.SUH REVDAT 6 06-NOV-24 1RZL 1 REMARK REVDAT 5 09-AUG-23 1RZL 1 REMARK REVDAT 4 18-APR-18 1RZL 1 REMARK REVDAT 3 13-JUL-11 1RZL 1 VERSN REVDAT 2 24-FEB-09 1RZL 1 VERSN REVDAT 1 16-DEC-98 1RZL 0 JRNL AUTH J.Y.LEE,K.MIN,H.CHA,D.H.SHIN,K.Y.HWANG,S.W.SUH JRNL TITL RICE NON-SPECIFIC LIPID TRANSFER PROTEIN: THE 1.6 A CRYSTAL JRNL TITL 2 STRUCTURE IN THE UNLIGANDED STATE REVEALS A SMALL JRNL TITL 3 HYDROPHOBIC CAVITY. JRNL REF J.MOL.BIOL. V. 276 437 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9512714 JRNL DOI 10.1006/JMBI.1997.1550 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.Y.HWANG,K.K.KIM,K.MIN,S.H.EOM,Y.G.YU,S.KIM,R.M.SWEET, REMARK 1 AUTH 2 S.W.SUH REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF PROBABLE AMYLASE/PROTEASE INHIBITOR-B FROM RICE REMARK 1 TITL 3 SEEDS REMARK 1 REF J.MOL.BIOL. V. 229 255 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 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) (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 9394 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) : 0.186 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 993 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.67 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 863 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 92 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 : 616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 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) : 0.017 REMARK 3 BOND ANGLES (DEGREES) : 1.760 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.770 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 : RLTP.PAR REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : RLTP.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-92 REMARK 200 TEMPERATURE (KELVIN) : 290 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 5 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 RUH2R 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 : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNES REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9447 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05500 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.1 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: 1MZL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.93500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.96500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.40250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.96500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.46750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.96500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.40250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.96500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.96500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.46750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.93500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 97.87000 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CXS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CXS A 211 DBREF 1RZL A 1 91 UNP P23096 NLTP1_ORYSA 1 91 SEQRES 1 A 91 ILE THR CYS GLY GLN VAL ASN SER ALA VAL GLY PRO CYS SEQRES 2 A 91 LEU THR TYR ALA ARG GLY GLY ALA GLY PRO SER ALA ALA SEQRES 3 A 91 CYS CYS SER GLY VAL ARG SER LEU LYS ALA ALA ALA SER SEQRES 4 A 91 THR THR ALA ASP ARG ARG THR ALA CYS ASN CYS LEU LYS SEQRES 5 A 91 ASN ALA ALA ARG GLY ILE LYS GLY LEU ASN ALA GLY ASN SEQRES 6 A 91 ALA ALA SER ILE PRO SER LYS CYS GLY VAL SER VAL PRO SEQRES 7 A 91 TYR THR ILE SER ALA SER ILE ASP CYS SER ARG VAL SER HET SO4 A 216 5 HET CXS A 201 14 HET CXS A 211 14 HETNAM SO4 SULFATE ION HETNAM CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID FORMUL 2 SO4 O4 S 2- FORMUL 3 CXS 2(C9 H19 N O3 S) FORMUL 5 HOH *68(H2 O) HELIX 1 1 CYS A 3 ALA A 17 1 15 HELIX 2 2 ALA A 25 ALA A 37 1 13 HELIX 3 3 THR A 41 ARG A 56 1 16 HELIX 4 4 ALA A 63 CYS A 73 1 11 SSBOND 1 CYS A 3 CYS A 50 1555 1555 2.02 SSBOND 2 CYS A 13 CYS A 27 1555 1555 2.01 SSBOND 3 CYS A 28 CYS A 73 1555 1555 2.02 SSBOND 4 CYS A 48 CYS A 87 1555 1555 2.01 CISPEP 1 GLY A 22 PRO A 23 0 -0.50 SITE 1 AC1 8 THR A 2 GLY A 4 SER A 24 ALA A 26 SITE 2 AC1 8 SER A 71 HOH A 101 HOH A 104 HOH A 154 SITE 1 AC2 9 PRO A 23 LYS A 72 SER A 84 ILE A 85 SITE 2 AC2 9 ASP A 86 ARG A 89 HOH A 111 HOH A 152 SITE 3 AC2 9 CXS A 211 SITE 1 AC3 8 ALA A 21 GLY A 22 PRO A 23 PRO A 78 SITE 2 AC3 8 ARG A 89 HOH A 102 HOH A 105 CXS A 201 CRYST1 37.930 37.930 97.870 90.00 90.00 90.00 P 43 21 2 8 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 0.026364 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010218 0.00000