PDB Short entry for 1IKT HEADER OXIDOREDUCTASE 07-MAY-01 1IKT TITLE LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN TITLE 2 MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ESTRADIOL 17 BETA-DEHYDROGENASE 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 618-736; COMPND 5 SYNONYM: HUMAN MULTIFUNCTIONAL ENZYME TYPE 2, MFE-2; COMPND 6 EC: 1.1.1.62; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HSD17B4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS ALFA-BETA FOLD, PROTEIN-TRITON X-100 COMPLEX, HYDROPHOBIC TUNNEL, KEYWDS 2 EXPOSED PEROXISOMAL TARGETING SIGNAL TYPE 1 (PTS1), OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.M.HAAPALAINEN,D.M.F.VAN AALTEN,T.GLUMOFF REVDAT 4 16-AUG-23 1IKT 1 REMARK SEQADV REVDAT 3 24-FEB-09 1IKT 1 VERSN REVDAT 2 01-APR-03 1IKT 1 JRNL REVDAT 1 14-NOV-01 1IKT 0 JRNL AUTH A.M.HAAPALAINEN,D.M.VAN AALTEN,G.MERILAINEN,J.E.JALONEN, JRNL AUTH 2 P.PIRILA,R.K.WIERENGA,J.K.HILTUNEN,T.GLUMOFF JRNL TITL CRYSTAL STRUCTURE OF THE LIGANDED SCP-2-LIKE DOMAIN OF HUMAN JRNL TITL 2 PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 2 AT 1.75 A JRNL TITL 3 RESOLUTION. JRNL REF J.MOL.BIOL. V. 313 1127 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11700068 JRNL DOI 10.1006/JMBI.2001.5084 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 495 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 : 9 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1196 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 60 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 : 898 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.30 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.509 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.507 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.087 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013373. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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 : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL FOCUSSING REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : PREMIRROR, BENT MIRROR REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 11659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : 0.03100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25900 REMARK 200 R SYM FOR SHELL (I) : 0.25900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1C44 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CHLORIDE, REMARK 280 TRITON X-100, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 17.73700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.36250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.01400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.36250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.73700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.01400 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 4 REMARK 465 LYS A 5 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 43 OD1 ND2 REMARK 480 GLN A 108 NE2 REMARK 480 LEU A 120 C O 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 LYS A 119 31.91 -167.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 OXN A 123 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 SO4 A 122 REMARK 615 OXN A 123 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 121 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 122 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXN A 123 DBREF 1IKT A 2 120 UNP P51659 DHB4_HUMAN 618 736 SEQADV 1IKT MET A 1 UNP P51659 CLONING ARTIFACT SEQRES 1 A 120 MET GLU GLY GLY LYS LEU GLN SER THR PHE VAL PHE GLU SEQRES 2 A 120 GLU ILE GLY ARG ARG LEU LYS ASP ILE GLY PRO GLU VAL SEQRES 3 A 120 VAL LYS LYS VAL ASN ALA VAL PHE GLU TRP HIS ILE THR SEQRES 4 A 120 LYS GLY GLY ASN ILE GLY ALA LYS TRP THR ILE ASP LEU SEQRES 5 A 120 LYS SER GLY SER GLY LYS VAL TYR GLN GLY PRO ALA LYS SEQRES 6 A 120 GLY ALA ALA ASP THR THR ILE ILE LEU SER ASP GLU ASP SEQRES 7 A 120 PHE MET GLU VAL VAL LEU GLY LYS LEU ASP PRO GLN LYS SEQRES 8 A 120 ALA PHE PHE SER GLY ARG LEU LYS ALA ARG GLY ASN ILE SEQRES 9 A 120 MET LEU SER GLN LYS LEU GLN MET ILE LEU LYS ASP TYR SEQRES 10 A 120 ALA LYS LEU HET SO4 A 121 5 HET SO4 A 122 5 HET OXN A 123 25 HETNAM SO4 SULFATE ION HETNAM OXN OXTOXYNOL-10 HETSYN OXN ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA- HETSYN 2 OXN HYDROXYPOLY(OXY-1,2-ETHANEDIYL); TRITON X-100 FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 OXN C34 H62 O11 FORMUL 5 HOH *126(H2 O) HELIX 1 1 GLN A 7 GLY A 23 1 17 HELIX 2 2 ILE A 22 ASN A 31 1 10 HELIX 3 3 ASP A 76 LEU A 84 1 9 HELIX 4 4 ASP A 88 SER A 95 1 8 HELIX 5 5 ASN A 103 ALA A 118 1 16 SHEET 1 A 5 LYS A 58 GLN A 61 0 SHEET 2 A 5 ILE A 44 LEU A 52 -1 N THR A 49 O TYR A 60 SHEET 3 A 5 ALA A 32 THR A 39 -1 O ALA A 32 N LEU A 52 SHEET 4 A 5 THR A 70 SER A 75 1 O THR A 70 N GLU A 35 SHEET 5 A 5 LYS A 99 GLY A 102 -1 N LYS A 99 O ILE A 73 SITE 1 AC1 4 ARG A 101 GLY A 102 HOH A1048 HOH A1125 SITE 1 AC2 2 GLU A 14 HOH A1311 SITE 1 AC3 9 TRP A 36 PRO A 89 GLN A 90 PHE A 93 SITE 2 AC3 9 MET A 105 SER A 107 GLN A 108 GLN A 111 SITE 3 AC3 9 LEU A 114 CRYST1 35.474 50.028 62.725 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 0.028190 -0.000001 -0.000001 0.00000 SCALE2 0.000000 0.019989 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.015943 0.00000