HEADER LIPID BINDING PROTEIN 09-JUL-03 1PZ4 TITLE THE STRUCTURAL DETERMINATION OF AN INSECT (MOSQUITO) STEROL CARRIER TITLE 2 PROTEIN-2 WITH A LIGAND BOUND C16 FATTY ACID AT 1.35 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROL CARRIER PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEDES AEGYPTI; SOURCE 3 ORGANISM_COMMON: YELLOW FEVER MOSQUITO; SOURCE 4 ORGANISM_TAXID: 7159; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEX-4T-2 GST KEYWDS ALPHA AND BETA, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.H.DYER,S.LOVELL,J.B.THODEN,H.M.HOLDEN,I.RAYMENT,Q.LAN REVDAT 4 14-FEB-24 1PZ4 1 REMARK SEQADV REVDAT 3 24-FEB-09 1PZ4 1 VERSN REVDAT 2 14-OCT-03 1PZ4 1 JRNL REVDAT 1 30-SEP-03 1PZ4 0 JRNL AUTH D.H.DYER,S.LOVELL,J.B.THODEN,H.M.HOLDEN,I.RAYMENT,Q.LAN JRNL TITL THE STRUCTURAL DETERMINATION OF AN INSECT STEROL CARRIER JRNL TITL 2 PROTEIN-2 WITH A LIGAND-BOUND C16 FATTY ACID AT 1.35A JRNL TITL 3 RESOLUTION JRNL REF J.BIOL.CHEM. V. 278 39085 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12855689 JRNL DOI 10.1074/JBC.M306214200 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 21157 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2107 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21157 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.012 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.230 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 16.600; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PZ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 7.5 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) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : BRUKER X1000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT, SMART REMARK 200 DATA SCALING SOFTWARE : SAINT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21157 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M SODIUM MALONATE, 100 MM TRIS-HCL, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 14.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.20000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.20000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.05000 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 PRO A -3 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 GLU A 83 CD GLU A 83 OE2 0.078 REMARK 500 GLU A 91 CD GLU A 91 OE2 0.067 REMARK 500 GLU A 103 CD GLU A 103 OE2 0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 20 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 20 CB - CG - OD2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASN A 43 CB - CA - C ANGL. DEV. = -12.3 DEGREES REMARK 500 ASP A 47 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 57 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 58 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 68 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 88 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES 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 GLU A 27 71.66 -118.27 REMARK 500 VAL A 51 70.27 72.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 200 DBREF 1PZ4 A 1 110 UNP Q86PR3 Q86PR3_AEDAE 1 110 SEQADV 1PZ4 GLY A -5 UNP Q86PR3 CLONING ARTIFACT SEQADV 1PZ4 SER A -4 UNP Q86PR3 CLONING ARTIFACT SEQADV 1PZ4 PRO A -3 UNP Q86PR3 CLONING ARTIFACT SEQADV 1PZ4 GLY A -2 UNP Q86PR3 CLONING ARTIFACT SEQADV 1PZ4 ILE A -1 UNP Q86PR3 CLONING ARTIFACT SEQADV 1PZ4 ARG A 0 UNP Q86PR3 CLONING ARTIFACT SEQRES 1 A 116 GLY SER PRO GLY ILE ARG MET SER LEU LYS SER ASP GLU SEQRES 2 A 116 VAL PHE ALA LYS ILE ALA LYS ARG LEU GLU SER ILE ASP SEQRES 3 A 116 PRO ALA ASN ARG GLN VAL GLU HIS VAL TYR LYS PHE ARG SEQRES 4 A 116 ILE THR GLN GLY GLY LYS VAL VAL LYS ASN TRP VAL MET SEQRES 5 A 116 ASP LEU LYS ASN VAL LYS LEU VAL GLU SER ASP ASP ALA SEQRES 6 A 116 ALA GLU ALA THR LEU THR MET GLU ASP ASP ILE MET PHE SEQRES 7 A 116 ALA ILE GLY THR GLY ALA LEU PRO ALA LYS GLU ALA MET SEQRES 8 A 116 ALA GLN ASP LYS MET GLU VAL ASP GLY GLN VAL GLU LEU SEQRES 9 A 116 ILE PHE LEU LEU GLU PRO PHE ILE ALA SER LEU LYS HET PLM A 200 18 HETNAM PLM PALMITIC ACID FORMUL 2 PLM C16 H32 O2 FORMUL 3 HOH *88(H2 O) HELIX 1 1 LYS A 4 GLU A 17 1 14 HELIX 2 2 ASP A 68 THR A 76 1 9 HELIX 3 3 PRO A 80 GLN A 87 1 8 HELIX 4 4 VAL A 96 LEU A 109 5 14 SHEET 1 A 5 LYS A 52 GLU A 55 0 SHEET 2 A 5 LYS A 39 ASP A 47 -1 N VAL A 45 O VAL A 54 SHEET 3 A 5 VAL A 29 GLN A 36 -1 N TYR A 30 O MET A 46 SHEET 4 A 5 ALA A 62 GLU A 67 1 O LEU A 64 N LYS A 31 SHEET 5 A 5 MET A 90 GLY A 94 -1 O GLU A 91 N THR A 65 SITE 1 AC1 7 ARG A 24 GLN A 25 VAL A 26 ILE A 99 SITE 2 AC1 7 PHE A 105 HOH A 412 HOH A 422 CRYST1 29.300 46.100 70.400 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 0.034130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021692 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014205 0.00000