HEADER OXIDOREDUCTASE 04-OCT-99 1D4O TITLE CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 ANGSTROMS TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADP(H) TRANSHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NADP(H) BINDING DOMAIN; COMPND 5 EC: 1.6.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 CELLULAR_LOCATION: MITOCHONDRIA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDE-BINDING FOLD, PROTEIN-NADP(H) COMPLEX, INVERTED BINDING OF KEYWDS 2 NADP(H), OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.S.PRASAD,V.SRIDHAR,M.YAMAGUCHI,Y.HATEFI,C.D.STOUT REVDAT 5 07-FEB-24 1D4O 1 REMARK REVDAT 4 31-JAN-18 1D4O 1 REMARK REVDAT 3 24-FEB-09 1D4O 1 VERSN REVDAT 2 23-MAY-00 1D4O 1 JRNL REVDAT 1 20-JAN-00 1D4O 0 JRNL AUTH G.S.PRASAD,V.SRIDHAR,M.YAMAGUCHI,Y.HATEFI,C.D.STOUT JRNL TITL CRYSTAL STRUCTURE OF TRANSHYDROGENASE DOMAIN III AT 1.2 A JRNL TITL 2 RESOLUTION. JRNL REF NAT.STRUCT.BIOL. V. 6 1126 1999 JRNL REFN ISSN 1072-8368 JRNL PMID 10581554 JRNL DOI 10.1038/70067 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.167 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.167 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1383 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 45717 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1338 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 185 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 1.700 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED SHELX LEAST SQUARES PROCEDURE. REMARK 4 REMARK 4 1D4O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009788. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45717 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 54.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 72.3 REMARK 200 DATA REDUNDANCY IN SHELL : 91.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 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: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% W/V MPEG 5000, 100MM SODIUM REMARK 280 CACODYLATE AND 200MM MAGNESIUM ACETATE., PH 7.4, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 ILE A 3 REMARK 465 SER A 4 REMARK 465 TYR A 182 REMARK 465 GLN A 183 REMARK 465 LYS A 184 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 ARG A 20 CD NE NH1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 343 O HOH A 450 1556 2.19 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 12 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 179 CD - NE - CZ ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 5.9 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 ASN A 107 -71.04 -153.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 201 DBREF 1D4O A 1 184 UNP P11024 NNTM_BOVIN 903 1086 SEQRES 1 A 184 MET GLU ILE SER GLY THR HIS THR GLU ILE ASN LEU ASP SEQRES 2 A 184 ASN ALA ILE ASP MET ILE ARG GLU ALA ASN SER ILE ILE SEQRES 3 A 184 ILE THR PRO GLY TYR GLY LEU CYS ALA ALA LYS ALA GLN SEQRES 4 A 184 TYR PRO ILE ALA ASP LEU VAL LYS MET LEU SER GLU GLN SEQRES 5 A 184 GLY LYS LYS VAL ARG PHE GLY ILE HIS PRO VAL ALA GLY SEQRES 6 A 184 ARG MET PRO GLY GLN LEU ASN VAL LEU LEU ALA GLU ALA SEQRES 7 A 184 GLY VAL PRO TYR ASP ILE VAL LEU GLU MET ASP GLU ILE SEQRES 8 A 184 ASN HIS ASP PHE PRO ASP THR ASP LEU VAL LEU VAL ILE SEQRES 9 A 184 GLY ALA ASN ASP THR VAL ASN SER ALA ALA GLN GLU ASP SEQRES 10 A 184 PRO ASN SER ILE ILE ALA GLY MET PRO VAL LEU GLU VAL SEQRES 11 A 184 TRP LYS SER LYS GLN VAL ILE VAL MET LYS ARG SER LEU SEQRES 12 A 184 GLY VAL GLY TYR ALA ALA VAL ASP ASN PRO ILE PHE TYR SEQRES 13 A 184 LYS PRO ASN THR ALA MET LEU LEU GLY ASP ALA LYS LYS SEQRES 14 A 184 THR CYS ASP ALA LEU GLN ALA LYS VAL ARG GLU SER TYR SEQRES 15 A 184 GLN LYS HET NAP A 201 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 HOH *185(H2 O) HELIX 1 1 ASN A 11 ALA A 22 1 12 HELIX 2 2 GLY A 30 ALA A 36 1 7 HELIX 3 3 ALA A 38 GLN A 52 1 15 HELIX 4 4 GLY A 69 GLY A 79 1 11 HELIX 5 5 PRO A 81 ASP A 83 5 3 HELIX 6 6 MET A 88 ASN A 92 1 5 HELIX 7 7 HIS A 93 THR A 98 5 6 HELIX 8 8 ASN A 107 ASN A 111 5 5 HELIX 9 9 SER A 112 ASP A 117 1 6 HELIX 10 10 GLU A 129 SER A 133 5 5 HELIX 11 11 ASN A 152 LYS A 157 5 6 HELIX 12 12 ASP A 166 GLU A 180 1 15 SHEET 1 A 6 VAL A 85 GLU A 87 0 SHEET 2 A 6 LYS A 55 ILE A 60 1 O PHE A 58 N LEU A 86 SHEET 3 A 6 SER A 24 PRO A 29 1 N ILE A 25 O LYS A 55 SHEET 4 A 6 LEU A 100 ILE A 104 1 O LEU A 100 N ILE A 26 SHEET 5 A 6 VAL A 136 LYS A 140 1 O ILE A 137 N VAL A 103 SHEET 6 A 6 THR A 160 LEU A 164 1 O ALA A 161 N VAL A 138 SITE 1 AC1 31 ASN A 23 GLY A 30 TYR A 31 GLY A 32 SITE 2 AC1 31 ALA A 35 ALA A 36 VAL A 63 ALA A 64 SITE 3 AC1 31 GLY A 65 ARG A 66 MET A 67 PRO A 68 SITE 4 AC1 31 GLY A 105 ALA A 106 ASN A 107 ASP A 108 SITE 5 AC1 31 THR A 109 LYS A 140 ARG A 141 SER A 142 SITE 6 AC1 31 VAL A 145 GLY A 146 TYR A 147 ASP A 166 SITE 7 AC1 31 ALA A 167 HOH A 314 HOH A 326 HOH A 353 SITE 8 AC1 31 HOH A 357 HOH A 366 HOH A 442 CRYST1 33.660 36.730 38.490 68.36 87.99 74.80 P 1 1 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 0.029734 -0.008028 0.002100 0.00000 SCALE2 0.000000 0.028201 -0.011328 0.00000 SCALE3 0.000000 0.000000 0.028013 0.00000