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- PDB-2nad: HIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 2nad
TitleHIGH RESOLUTION STRUCTURES OF HOLO AND APO FORMATE DEHYDROGENASE
ComponentsNAD-DEPENDENT FORMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(ALDEHYDE(D) / NAD+(A))
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain ...NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsLamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: High resolution structures of holo and apo formate dehydrogenase.
Authors: Lamzin, V.S. / Dauter, Z. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
#1: Journal: Eur.J.Biochem. / Year: 1992
Title: Crystal Structure of Nad-Dependent Formate Dehydrogenase
Authors: Lamzin, V.S. / Aleshin, A.E. / Strokopytov, B.V. / Yukhnevich, M.G. / Popov, V.O. / Harutyunyan, E.H. / Wilson, K.S.
History
DepositionJul 6, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-DEPENDENT FORMATE DEHYDROGENASE
B: NAD-DEPENDENT FORMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0817
Polymers86,5742
Non-polymers1,5075
Water14,970831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-71 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.970, 113.290, 63.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO A 312 / 2: CIS PROLINE - PRO A 314 / 3: CIS PROLINE - PRO B 312 / 4: CIS PROLINE - PRO B 314
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.71486, -0.62783, -0.3079), (-0.62588, 0.37811, 0.68213), (-0.31184, 0.68034, -0.66325)
Vector: 98.653, 38.406, 13.063)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein NAD-DEPENDENT FORMATE DEHYDROGENASE


Mass: 43286.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: 101 / References: UniProt: P33160, formate dehydrogenase
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_ ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: FDH_PSESR SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 77 ASP A 77 VAL 138 THR A 138 THR 139 VAL A 139 VAL 145 CYS A 145 HIS 215 VAL A 215 VAL 216 HIS A 216 ASP 327 ASN A 327 SER 77 ASP B 77 VAL 138 THR B 138 THR 139 VAL B 139 VAL 145 CYS B 145 HIS 215 VAL B 215 VAL 216 HIS B 216 ASP 327 ASN B 327 THERE IS ALSO THE GENE SEQUENCE OF THE PSEUDOMONAS SP. 101 FORMATE DEHYDROGENASE AVAILABLE (TISHKOV ET AL., 1991, DOKL. ACAD. NAUK USSR (USSR), 317, 745 - 748), WHICH AGREES WITH THE COORDINATE SET. THIS HAS BEEN DISCUSSED IN THE PAPER CITED ON JRNL RECORDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 %ammonium sulfate1reservoirprecipitant
25 %MPD1reservoir
35 mMNAD1reservoir
45 mMsodium azide1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 51142 / % possible obs: 90.3 % / Observed criterion σ(I): 3 / Num. measured all: 206376 / Rmerge(I) obs: 0.045 / Biso Wilson estimate: 11.1 Å2
Reflection shell
*PLUS
% possible obs: 84.7 % / Rmerge(I) obs: 0.075

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Processing

Software
NameClassification
ARP/wARPmodel building
PROLSQrefinement
RefinementResolution: 2.05→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.114 50775
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 99 831 6943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0450.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.592
X-RAY DIFFRACTIONp_mcangle_it2.273
X-RAY DIFFRACTIONp_scbond_it4.834
X-RAY DIFFRACTIONp_scangle_it6.955
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.1680.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2160.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.933
X-RAY DIFFRACTIONp_staggered_tor15.4115
X-RAY DIFFRACTIONp_orthonormal_tor32.2920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/ARP / Classification: refinement
Refinement
*PLUS
Num. reflection all: 50775 / Rfactor all: 0.114
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.4 Å2

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