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- PDB-1civ: CHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS -

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Basic information

Entry
Database: PDB / ID: 1civ
TitleCHLOROPLAST NADP-DEPENDENT MALATE DEHYDROGENASE FROM FLAVERIA BIDENTIS
ComponentsNADP-MALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHLOROPLAST / LIGHT ACTIVATED / NADP-DEPENDENT / DEHYDROGENASE
Function / homology
Function and homology information


malate dehydrogenase (NADP+) / L-malate dehydrogenase (NADP+) activity / malate metabolic process / chloroplast
Similarity search - Function
Malate dehydrogenase, NADP-dependent, plants / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...Malate dehydrogenase, NADP-dependent, plants / Malate dehydrogenase, type 2 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Malate dehydrogenase [NADP], chloroplastic
Similarity search - Component
Biological speciesFlaveria bidentis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.8 Å
AuthorsCarr, P.D. / Ashton, A.R. / Verger, D. / Ollis, D.L.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Chloroplast NADP-malate dehydrogenase: structural basis of light-dependent regulation of activity by thiol oxidation and reduction.
Authors: Carr, P.D. / Verger, D. / Ashton, A.R. / Ollis, D.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary crystallographic studies of chloroplast NADP-dependent malate dehydrogenase from Flaveria bidentis.
Authors: MacPherson, K.H. / Ashton, A.R. / Carr, P.D. / Trevanion, S.J. / Verger, D. / Ollis, D.L.
History
DepositionApr 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.6Aug 9, 2023Group: 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
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8402
Polymers42,0971
Non-polymers7431
Water1,910106
1
A: NADP-MALATE DEHYDROGENASE
hetero molecules

A: NADP-MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6814
Polymers84,1942
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+4/31
Buried area7020 Å2
ΔGint-34 kcal/mol
Surface area27140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.800, 147.800, 64.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NADP-MALATE DEHYDROGENASE


Mass: 42097.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DARKENED LEAVES / Source: (natural) Flaveria bidentis (plant) / Organ: LEAF / Organelle: CHLOROPLAST / References: UniProt: P46489, malate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.8 Å3/Da / Density % sol: 74.68 %
Description: BOTH SIRAS AND MOLECULAR REPLACEMENT METHODS WERE USED
Crystal growpH: 7.5
Details: SEE MACPHERSON ET AL. (1998) ACTA CRYST, D54, 654 - 656, pH 7.50
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 Mammonium sulfate11
20.1 MHEPES11
312 %glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 20335 / % possible obs: 98.3 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.132
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 98.3 % / Observed criterion σ(I): 4 / Redundancy: 1.9 % / Num. measured all: 38553

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
X-PLOR3.84refinement
CCP4phasing
RefinementMethod to determine structure: SIRAS
Starting model: 4MDH

4mdh


Resolution: 2.8→15 Å / Data cutoff low absF: 250 / Cross valid method: R-FREE / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.284 -5 %RANDOM
Rwork0.205 ---
obs-17473 84.75 %-
Refine analyzeLuzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 48 106 2959
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.78→2.88 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.372 54 5 %
Rwork0.264 1096 -
obs--56.81 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADPTOP.NADP
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.372 / Rfactor Rwork: 0.264

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