PDB Short entry for 1C44 HEADER LIPID BINDING PROTEIN 02-JUL-99 1C44 TITLE STEROL CARRIER PROTEIN 2 (SCP2) FROM RABBIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (STEROL CARRIER PROTEIN 2); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON SPECIFIC LIPID BINDING PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 ORGAN: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS STEROL CARRIER PROTEIN, NON SPECIFIC LIPID TRANSFER PROTEIN, FATTY KEYWDS 2 ACID BINDING, FATTY ACYL COA BINDING, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.CHOINOWSKI,H.HAUSER,K.PIONTEK REVDAT 3 27-DEC-23 1C44 1 REMARK SEQADV REVDAT 2 24-FEB-09 1C44 1 VERSN REVDAT 1 07-AUG-00 1C44 0 JRNL AUTH T.CHOINOWSKI,H.HAUSER,K.PIONTEK JRNL TITL STRUCTURE OF STEROL CARRIER PROTEIN 2 AT 1.8 A RESOLUTION JRNL TITL 2 REVEALS A HYDROPHOBIC TUNNEL SUITABLE FOR LIPID BINDING. JRNL REF BIOCHEMISTRY V. 39 1897 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10684638 JRNL DOI 10.1021/BI992742E REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.CHOINOWSKI,J.H.DYER,B.MADEREGGER,K.P.WINTERHALTER, REMARK 1 AUTH 2 H.HAUSER,K.PIONTEK REMARK 1 TITL CRYSTALLIZATION AND INITIAL X-RAY ANALYSIS OF RABBIT MATURE REMARK 1 TITL 2 STEROL CARRIER PROTEIN 2 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1478 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999007106 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 13993 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 693 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.190 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.017 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.032 ; 0.035 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.038 ; 0.040 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.020 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.146 ; 0.140 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.197 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.301 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.199 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.600 ; 5.000 REMARK 3 STAGGERED (DEGREES) : 16.200; 10.000 REMARK 3 TRANSVERSE (DEGREES) : 17.000; 15.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.868 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.691 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.430 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.004 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1C44 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-99. REMARK 100 THE DEPOSITION ID IS D_1000001280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8345 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 4.90000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 36.2000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, LITHIUM SULFATE, REMARK 280 CITRATE PH=6.5, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 43.24350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.74300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.74300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.62175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.74300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.74300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.86525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.74300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.74300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.62175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.74300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.74300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.86525 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 43.24350 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 124 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 125 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 GLN A 115 N GLN A 117 1.71 REMARK 500 C GLN A 115 N GLN A 117 1.87 REMARK 500 O LEU A 83 O LEU A 116 2.18 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 LEU A 114 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 ALA A 121 O - C - N ANGL. DEV. = 15.8 DEGREES REMARK 500 LYS A 122 CA - C - N ANGL. DEV. = -16.3 DEGREES REMARK 500 LYS A 122 O - C - N ANGL. DEV. = 19.5 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 ILE A 31 -70.39 -99.79 REMARK 500 LEU A 114 -2.10 -58.59 REMARK 500 GLN A 115 -175.61 105.60 REMARK 500 LEU A 116 -13.88 -27.56 REMARK 500 GLN A 117 32.85 105.42 REMARK 500 LYS A 120 53.18 37.59 REMARK 500 LYS A 122 93.80 -31.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 1C44 A 1 123 UNP O62742 NLTP_RABIT 425 547 SEQADV 1C44 MET A 75 UNP O62742 ILE 499 CONFLICT SEQRES 1 A 123 SER SER ALA GLY ASP GLY PHE LYS ALA ASN LEU VAL PHE SEQRES 2 A 123 LYS GLU ILE GLU LYS LYS LEU GLU GLU GLU GLY GLU GLN SEQRES 3 A 123 PHE VAL LYS LYS ILE GLY GLY ILE PHE ALA PHE LYS VAL SEQRES 4 A 123 LYS ASP GLY PRO GLY GLY LYS GLU ALA THR TRP VAL VAL SEQRES 5 A 123 ASP VAL LYS ASN GLY LYS GLY SER VAL LEU PRO ASN SER SEQRES 6 A 123 ASP LYS LYS ALA ASP CYS THR ILE THR MET ALA ASP SER SEQRES 7 A 123 ASP LEU LEU ALA LEU MET THR GLY LYS MET ASN PRO GLN SEQRES 8 A 123 SER ALA PHE PHE GLN GLY LYS LEU LYS ILE THR GLY ASN SEQRES 9 A 123 MET GLY LEU ALA MET LYS LEU GLN ASN LEU GLN LEU GLN SEQRES 10 A 123 PRO GLY LYS ALA LYS LEU FORMUL 2 HOH *140(H2 O) HELIX 1 A PHE A 7 GLU A 22 1 16 HELIX 2 B GLU A 23 ILE A 31 1 9 HELIX 3 C GLY A 42 LYS A 46 5 5 HELIX 4 D ASP A 77 THR A 85 1 9 HELIX 5 E ASN A 89 GLN A 96 1 8 HELIX 6 F ASN A 104 ASN A 113 1 10 SHEET 1 I 1 GLY A 33 LYS A 40 0 SHEET 1 II 1 ALA A 48 VAL A 54 0 SHEET 1 III 1 SER A 60 PRO A 63 0 SHEET 1 IV 1 CYS A 71 ALA A 76 0 SHEET 1 V 1 LYS A 100 GLY A 103 0 CRYST1 57.486 57.486 86.487 90.00 90.00 90.00 P 41 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 0.017395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017395 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011562 0.00000