HEADER PROTEIN TRANSPORT/OXIDOREDUCTASE 15-NOV-04 1WT4 OBSLTE 12-JUN-07 1WT4 2V1T TITLE CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20 COMPND 3 HOMOLOG; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: CYTOSOLIC DOMAIN, LIMITED PROTEOLYZED FRAGMENT; COMPND 6 SYNONYM: MITOCHONDRIAL 20 KDA OUTER MEMBRANE PROTEIN, COMPND 7 OUTER MITOCHONDRIAL MEMBRANE RECEPTOR TOM20; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ALDEHYDE DEHYDROGENASE, MITOCHONDRIAL; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: C-TERMINAL HALF OF THE PRESEQUENCE OF COMPND 13 MITOCHONDRIAL PRECURSOR; COMPND 14 SYNONYM: ALDH CLASS 2, ALDH1, ALDH-E2; COMPND 15 EC: 1.2.1.3; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: ALDH-PRE SEQUENCE KEYWDS PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.OBITA,M.IGURA,T.OSE,T.ENDO,K.MAENAKA,D.KOHDA REVDAT 2 12-JUN-07 1WT4 1 OBSLTE REVDAT 1 22-NOV-05 1WT4 0 JRNL AUTH T.OBITA,M.IGURA,T.OSE,T.ENDO,K.MAENAKA,D.KOHDA JRNL TITL CRYSTAL STRUCTURE OF RAT TOM20-ALDH PRESEQUENCE JRNL TITL 2 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 9777 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) : 0.184 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 877 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2544 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 0 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 : 1279 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.26600 REMARK 3 B22 (A**2) : 0.59900 REMARK 3 B33 (A**2) : 4.66600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.70100 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.51 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.45 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.92 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 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: USED WEIGHTED FULL MATRIX LEAST REMARK 3 SQUARES PROCEDURE REMARK 4 REMARK 4 1WT4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.102 (2007-06-08) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE RCSB ID CODE IS RCSB023968. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-2004 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9838 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9958 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.16800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1OM2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, AMMONIUM CHLORIDE, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.82200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 B 54 REMARK 465 PRO B 55 REMARK 465 LEU B 56 REMARK 465 GLY B 57 REMARK 465 SER B 58 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 100 CA - CB - SG ANGL. DEV. = 9.7 DEGREES REMARK 500 LEU B 60 N - CA - C ANGL. DEV. = 9.6 DEGREES REMARK 500 PRO B 117 C - N - CD ANGL. DEV. = 9.6 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OM2 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE DBREF 1WT4 A 59 126 UNP Q62760 TOM20_RAT 59 126 DBREF 1WT4 B 59 126 UNP Q62760 TOM20_RAT 59 126 DBREF 1WT4 C 12 22 UNP P11884 ALDH2_RAT 12 22 DBREF 1WT4 D 12 22 UNP P11884 ALDH2_RAT 12 22 SEQADV 1WT4 GLY A 54 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 PRO A 55 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 LEU A 56 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 GLY A 57 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 SER A 58 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 MSE A 121 UNP Q62760 MET 121 MODIFIED RESIDUE SEQADV 1WT4 GLY B 54 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 PRO B 55 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 LEU B 56 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 GLY B 57 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 SER B 58 UNP Q62760 CLONING ARTIFACT SEQADV 1WT4 MSE B 121 UNP Q62760 MET 121 MODIFIED RESIDUE SEQADV 1WT4 GLY C 23 UNP P11884 ALA 23 ENGINEERED SEQADV 1WT4 CYS C 24 UNP P11884 CLONING ARTIFACT SEQADV 1WT4 GLY D 23 UNP P11884 ALA 23 ENGINEERED SEQADV 1WT4 CYS D 24 UNP P11884 CLONING ARTIFACT SEQRES 1 A 73 GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL SEQRES 2 A 73 GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU SEQRES 3 A 73 LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS SEQRES 4 A 73 LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN SEQRES 5 A 73 LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL SEQRES 6 A 73 PHE GLN MSE LEU LEU THR LYS LEU SEQRES 1 B 73 GLY PRO LEU GLY SER ASP LEU LYS ASP ALA GLU ALA VAL SEQRES 2 B 73 GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU GLY GLU GLU SEQRES 3 B 73 LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY VAL ASP HIS SEQRES 4 B 73 LEU THR ASN ALA ILE ALA VAL CYS GLY GLN PRO GLN GLN SEQRES 5 B 73 LEU LEU GLN VAL LEU GLN GLN THR LEU PRO PRO PRO VAL SEQRES 6 B 73 PHE GLN MSE LEU LEU THR LYS LEU SEQRES 1 C 13 GLY PRO ARG LEU SER ARG LEU LEU SER ALA ALA GLY CYS SEQRES 1 D 13 GLY PRO ARG LEU SER ARG LEU LEU SER ALA ALA GLY CYS MODRES 1WT4 MSE A 121 MET SELENOMETHIONINE MODRES 1WT4 MSE B 121 MET SELENOMETHIONINE HET MSE A 121 8 HET MSE B 121 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 5 HOH *152(H2 O) HELIX 1 1 ASP A 59 GLY A 84 1 26 HELIX 2 2 ASP A 85 VAL A 99 1 15 HELIX 3 3 PRO A 103 LEU A 114 1 12 HELIX 4 4 PRO A 115 LEU A 126 1 12 HELIX 5 5 GLU B 64 GLN B 83 1 20 HELIX 6 6 ASP B 85 VAL B 99 1 15 HELIX 7 7 PRO B 103 LEU B 114 1 12 HELIX 8 8 PRO B 115 LYS B 125 1 11 HELIX 9 9 LEU B 126 LEU B 126 5 1 HELIX 10 10 GLY C 12 ARG C 14 5 3 SSBOND 1 CYS A 100 CYS C 24 SSBOND 2 CYS B 100 CYS D 24 CRYST1 33.641 27.644 70.973 90.00 103.06 90.00 P 1 21 1 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 0.029726 0.000000 0.006895 0.00000 SCALE2 0.000000 0.036174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014464 0.00000