PDB Short entry for 1OR2 HEADER LIPID BINDING PROTEIN 25-MAR-99 1OR2 TITLE APOLIPOPROTEIN E3 (APOE3) TRUNCATION MUTANT 165 COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RECEPTOR BINDING DOMAIN, RESIDUES 1-165; COMPND 5 SYNONYM: APOE3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: SELENOMETHIONINE MUTANT USED IN MAD PHASING EXPERIMENT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: B834(DE)MET-; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE)MET-; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS LIPID TRANSPORT, HEPARIN-BINDING, PLASMA PROTEIN, HDL, VLDL, LIPID KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.RUPP,B.W.SEGELKE,M.FORSTNER REVDAT 7 15-NOV-23 1OR2 1 REMARK REVDAT 6 16-AUG-23 1OR2 1 SEQADV LINK REVDAT 5 04-OCT-17 1OR2 1 REMARK REVDAT 4 24-FEB-09 1OR2 1 VERSN REVDAT 3 01-APR-03 1OR2 1 JRNL REVDAT 2 23-MAY-00 1OR2 1 JRNL DBREF REVDAT 1 10-APR-00 1OR2 0 JRNL AUTH B.W.SEGELKE,M.FORSTNER,M.KNAPP,S.D.TRAKHANOV,S.PARKIN, JRNL AUTH 2 Y.M.NEWHOUSE,H.D.BELLAMY,K.H.WEISGRABER,B.RUPP JRNL TITL CONFORMATIONAL FLEXIBILITY IN THE APOLIPOPROTEIN E JRNL TITL 2 AMINO-TERMINAL DOMAIN STRUCTURE DETERMINED FROM THREE NEW JRNL TITL 3 CRYSTAL FORMS: IMPLICATIONS FOR LIPID BINDING. JRNL REF PROTEIN SCI. V. 9 886 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 10850798 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 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)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 5457 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) : 0.267 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 544 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.59 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 367 REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 40 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.059 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.72000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.44 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.45 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.030 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) : 3.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.220 ; 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 : PR REMARK 3 PARAMETER FILE 2 : TI REMARK 3 PARAMETER FILE 3 : SME_BONDS.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : METSE.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1OR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 125 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-SYSTEM DATA REDUCTION REMARK 200 PACKAGE REMARK 200 DATA SCALING SOFTWARE : UCSD-SYSTEM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 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 (%) : 93.8 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24500 REMARK 200 R SYM FOR SHELL (I) : 0.24500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR, X-PLOR, CCP4 REMARK 200 STARTING MODEL: 1BZ4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM NA-CACODYLATE, PH 5.6, 10-20% PEG REMARK 280 400 AT ROOM TEMPERATURE. NO 2-ME ADDED. NOTE: WITH 2-ME OR LOWER REMARK 280 PEG CONCENTRATIONS, OTHER CRYSTAL FORMS APPEARS (SEE PDB ENTRIES REMARK 280 1BZ4, 1OR3), 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 23.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.79500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.79500 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 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 SER A 22 REMARK 465 LEU A 82 REMARK 465 THR A 83 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 ALA A 91 REMARK 465 ARG A 92 REMARK 465 ALA A 164 REMARK 465 GLY A 165 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 MSE A 125 OE1 GLN A 128 2.13 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 GLN A 41 -37.73 -36.28 REMARK 500 SER A 54 33.32 73.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 1OR2 A 1 165 UNP P02649 APOE_HUMAN 19 183 SEQADV 1OR2 MSE A 64 UNP P02649 MET 82 MODIFIED RESIDUE SEQADV 1OR2 MSE A 68 UNP P02649 MET 86 MODIFIED RESIDUE SEQADV 1OR2 MSE A 108 UNP P02649 MET 126 MODIFIED RESIDUE SEQADV 1OR2 MSE A 125 UNP P02649 MET 143 MODIFIED RESIDUE 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 MSE ASP SEQRES 6 A 165 GLU THR MSE 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 MSE GLU ASP VAL CYS GLY ARG LEU VAL GLN SEQRES 10 A 165 TYR ARG GLY GLU VAL GLN ALA MSE 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 MODRES 1OR2 MSE A 64 MET SELENOMETHIONINE MODRES 1OR2 MSE A 68 MET SELENOMETHIONINE MODRES 1OR2 MSE A 108 MET SELENOMETHIONINE MODRES 1OR2 MSE A 125 MET SELENOMETHIONINE HET MSE A 64 8 HET MSE A 68 8 HET MSE A 108 8 HET MSE A 125 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 HOH *53(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 GLU A 80 1 27 HELIX 4 4 LYS A 95 GLN A 123 1 29 HELIX 5 5 THR A 130 GLN A 163 1 34 LINK C LEU A 63 N MSE A 64 1555 1555 1.33 LINK C MSE A 64 N ASP A 65 1555 1555 1.33 LINK C THR A 67 N MSE A 68 1555 1555 1.33 LINK C MSE A 68 N LYS A 69 1555 1555 1.33 LINK C ASP A 107 N MSE A 108 1555 1555 1.33 LINK C MSE A 108 N GLU A 109 1555 1555 1.33 LINK C ALA A 124 N MSE A 125 1555 1555 1.33 LINK C MSE A 125 N LEU A 126 1555 1555 1.33 CRYST1 47.680 55.590 63.590 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 0.020973 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017989 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015726 0.00000