10 20 30 40 50 60 70 80 1OR3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIPID BINDING PROTEIN 01-DEC-98 1OR3
TITLE APOLIPOPROTEIN E3 (APOE3), TRIGONAL TRUNCATION MUTANT 165
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (APOLIPOPROTEIN E); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 5 SYNONYM: APOE3; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SELENOMETHIONINE MUTANT USED IN MAD PHASING COMPND 8 EXPERIMENT
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: BL21, B834(DE)MET-; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21, B834(DE)MET-; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET
KEYWDS LIPID TRANSPORT, HEPARIN-BINDING, PLASMA PROTEIN, HDL, VLDL, KEYWDS 2 LIPID BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR B.RUPP,B.W.SEGELKE
REVDAT 3 24-FEB-09 1OR3 1 VERSN REVDAT 2 01-APR-03 1OR3 1 JRNL REVDAT 1 24-MAY-00 1OR3 0
JRNL AUTH B.W.SEGELKE,M.FORSTNER,M.KNAPP,S.D.TRAKHANOV, JRNL AUTH 2 S.PARKIN,Y.M.NEWHOUSE,H.D.BELLAMY,K.H.WEISGRABER, JRNL AUTH 3 B.RUPP JRNL TITL CONFORMATIONAL FLEXIBILITY IN THE APOLIPOPROTEIN E JRNL TITL 2 AMINO-TERMINAL DOMAIN STRUCTURE DETERMINED FROM JRNL TITL 3 THREE NEW CRYSTAL FORMS: IMPLICATIONS FOR LIPID JRNL TITL 4 BINDING. JRNL REF PROTEIN SCI. V. 9 886 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 10850798
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.9 REMARK 3 NUMBER OF REFLECTIONS : 13222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1339 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 112 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 967 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1148 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.23000 REMARK 3 B22 (A**2) : -1.23000 REMARK 3 B33 (A**2) : 2.46000 REMARK 3 B12 (A**2) : -3.35000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.59 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.620 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.100; 2.500 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 : PROTEIN_REP.PA REMARK 3 PARAMETER FILE 2 : TIP3P.PARAMETE REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4 REMARK 4 1OR3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-98. REMARK 100 THE RCSB ID CODE IS RCSB000187.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 125.0 REMARK 200 PH : 5.6 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 : GRAPHITE REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : UCSD REMARK 200 DATA SCALING SOFTWARE : UCSD REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16782 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 6.80000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.22500 REMARK 200 R SYM FOR SHELL (I) : 22.50000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, X-PLOR, CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: 4 WAVELENGTHS USED FOR PHASING (ALS BEAMLINE 5.0.2)
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RT, 50MM NA-CACODYLATE, PH 5.6, 10- REMARK 280 20% PEG 400, 1% 2-ME. NOTE: W/O 2-ME OR HIGHER PEG REMARK 280 CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES REMARK 280 1BZ4, 1OR2).
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.84667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.69333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.69333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.84667 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 NH2 ARG A 114 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 212 LIES ON A SPECIAL POSITION.
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 LYS A 1 REMARK 465 VAL A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 ALA A 5 REMARK 465 VAL A 6 REMARK 465 GLU A 7 REMARK 465 THR A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 GLU A 11 REMARK 465 PRO A 12 REMARK 465 GLU A 13 REMARK 465 LEU A 14 REMARK 465 ARG A 15 REMARK 465 GLN A 16 REMARK 465 GLN A 17 REMARK 465 THR A 18 REMARK 465 GLU A 19 REMARK 465 TRP A 20 REMARK 465 GLN A 21 REMARK 465 PRO A 84 REMARK 465 VAL A 85 REMARK 465 ALA A 86 REMARK 465 GLU A 87 REMARK 465 GLU A 88 REMARK 465 THR A 89 REMARK 465 ARG A 90 REMARK 465 GLY A 165
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 ARG A 114 CZ ARG A 114 NH2 0.093 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 214 DISTANCE = 8.44 ANGSTROMS REMARK 525 HOH A 225 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A 265 DISTANCE = 7.91 ANGSTROMS REMARK 525 HOH A 322 DISTANCE = 6.54 ANGSTROMS
DBREF 1OR3 A 1 165 UNP P02649 APOE_HUMAN 19 183
SEQRES 1 A 165 LYS VAL GLU GLN ALA VAL GLU THR GLU PRO GLU PRO GLU SEQRES 2 A 165 LEU ARG GLN GLN THR GLU TRP GLN SER GLY GLN ARG TRP SEQRES 3 A 165 GLU LEU ALA LEU GLY ARG PHE TRP ASP TYR LEU ARG TRP SEQRES 4 A 165 VAL GLN THR LEU SER GLU GLN VAL GLN GLU GLU LEU LEU SEQRES 5 A 165 SER SER GLN VAL THR GLN GLU LEU ARG ALA LEU MET ASP SEQRES 6 A 165 GLU THR MET LYS GLU LEU LYS ALA TYR LYS SER GLU LEU SEQRES 7 A 165 GLU GLU GLN LEU THR PRO VAL ALA GLU GLU THR ARG ALA SEQRES 8 A 165 ARG LEU SER LYS GLU LEU GLN ALA ALA GLN ALA ARG LEU SEQRES 9 A 165 GLY ALA ASP MET GLU ASP VAL CYS GLY ARG LEU VAL GLN SEQRES 10 A 165 TYR ARG GLY GLU VAL GLN ALA MET LEU GLY GLN SER THR SEQRES 11 A 165 GLU GLU LEU ARG VAL ARG LEU ALA SER HIS LEU ARG LYS SEQRES 12 A 165 LEU ARG LYS ARG LEU LEU ARG ASP ALA ASP ASP LEU GLN SEQRES 13 A 165 LYS ARG LEU ALA VAL TYR GLN ALA GLY
FORMUL 2 HOH *158(H2 O)
HELIX 1 1 GLN A 24 THR A 42 1 19 HELIX 2 2 SER A 44 SER A 53 1 10 HELIX 3 3 SER A 54 LEU A 82 1 29 HELIX 4 4 ALA A 91 GLN A 123 1 33 HELIX 5 5 THR A 130 GLN A 163 1 34
CRYST1 47.370 47.370 104.540 90.00 90.00 120.00 P 31 2 1 6
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 0.021110 0.012188 0.000000 0.00000
SCALE2 0.000000 0.024376 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009566 0.00000