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- PDB-4uup: Reconstructed ancestral trichomonad malate dehydrogenase in compl... -

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Basic information

Entry
Database: PDB / ID: 4uup
TitleReconstructed ancestral trichomonad malate dehydrogenase in complex with NADH, SO4, and PO4
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homologyL-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / PHOSPHATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å
AuthorsSteindel, P.A. / Chen, E.H. / Theobald, D.L.
CitationJournal: Protein Sci. / Year: 2016
Title: Gradual Neofunctionalization in the Convergent Evolution of Trichomonad Lactate and Malate Dehydrogenases.
Authors: Steindel, P.A. / Chen, E.H. / Wirth, J.D. / Theobald, D.L.
History
DepositionJul 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4046
Polymers73,8822
Non-polymers1,5224
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-58.9 kcal/mol
Surface area26060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.460, 58.850, 81.570
Angle α, β, γ (deg.)90.00, 111.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MALATE DEHYDROGENASE


Mass: 36941.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / References: malate dehydrogenase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDESIGNED SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE
Crystal growpH: 8
Details: 5 MG/ML PROTEIN, 100 MM TRIS, PH 8.0, 25% PEG 4000, AND 0.2M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.54→46.5 Å / Num. obs: 91959 / % possible obs: 93.6 % / Observed criterion σ(I): 0.65 / Redundancy: 8.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.59
Reflection shellResolution: 1.54→1.58 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 0.65 / Rsym value: 1.11 / % possible all: 58.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL BASED ON PDB ENTRY 5MDH

5mdh


Resolution: 1.543→46.539 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 4569 4.97 %
Rwork0.1667 --
obs0.1684 91936 93.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 1.543→46.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5053 0 98 598 5749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055406
X-RAY DIFFRACTIONf_angle_d1.027379
X-RAY DIFFRACTIONf_dihedral_angle_d12.3682009
X-RAY DIFFRACTIONf_chiral_restr0.054826
X-RAY DIFFRACTIONf_plane_restr0.004961
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5431-1.56060.451670.43111573X-RAY DIFFRACTION51
1.5606-1.5790.38121020.32931965X-RAY DIFFRACTION64
1.579-1.59820.34641020.29912161X-RAY DIFFRACTION69
1.5982-1.61840.28121170.27832282X-RAY DIFFRACTION74
1.6184-1.63970.34711440.26762475X-RAY DIFFRACTION80
1.6397-1.66220.31621340.25782618X-RAY DIFFRACTION85
1.6622-1.6860.29881380.2512867X-RAY DIFFRACTION92
1.686-1.71110.27441910.24292982X-RAY DIFFRACTION98
1.7111-1.73790.31661380.22763136X-RAY DIFFRACTION100
1.7379-1.76640.26871690.21333084X-RAY DIFFRACTION100
1.7664-1.79680.27051610.21293092X-RAY DIFFRACTION100
1.7968-1.82950.24881760.20533058X-RAY DIFFRACTION100
1.8295-1.86470.24171450.20813117X-RAY DIFFRACTION100
1.8647-1.90270.21951710.19693095X-RAY DIFFRACTION100
1.9027-1.94410.26451440.18773076X-RAY DIFFRACTION100
1.9441-1.98930.22681800.18573098X-RAY DIFFRACTION100
1.9893-2.03910.21711600.18753123X-RAY DIFFRACTION100
2.0391-2.09420.23641610.18273097X-RAY DIFFRACTION100
2.0942-2.15580.2111730.16843067X-RAY DIFFRACTION100
2.1558-2.22540.19611630.15923118X-RAY DIFFRACTION100
2.2254-2.3050.21761520.16583070X-RAY DIFFRACTION100
2.305-2.39720.22251660.15723110X-RAY DIFFRACTION100
2.3972-2.50630.2031510.1653108X-RAY DIFFRACTION100
2.5063-2.63850.21991640.16643114X-RAY DIFFRACTION100
2.6385-2.80380.19871660.17123139X-RAY DIFFRACTION100
2.8038-3.02020.20531690.1723088X-RAY DIFFRACTION100
3.0202-3.32410.20521530.16943133X-RAY DIFFRACTION100
3.3241-3.80490.19111720.14693136X-RAY DIFFRACTION100
3.8049-4.7930.15831680.12843172X-RAY DIFFRACTION100
4.793-46.56030.13171720.14423213X-RAY DIFFRACTION100

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