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- PDB-7mdh: STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. TH... -

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Basic information

Entry
Database: PDB / ID: 7mdh
TitleSTRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. THE STRUCTURE OF SORGHUM NADP-MALATE DEHYDROGENASE IN ITS OXIDIZED FORM
ComponentsPROTEIN (MALATE DEHYDROGENASE)
KeywordsCHLOROPLASTIC MALATE DEHYDROGENASE / CHLOROPLASTIC MALATE DEHYDROGENASE (NADP+) / ACTIVATED BY LIGHT
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
Malate dehydrogenase [NADP] 1, chloroplastic
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJohansson, K. / Ramaswamy, S. / Saarinen, M. / Lemaire-Chamley, M. / Issakidis-Bourguet, E. / Miginiac-Maslow, M. / Eklund, H.
CitationJournal: Biochemistry / Year: 1999
Title: Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form.
Authors: Johansson, K. / Ramaswamy, S. / Saarinen, M. / Lemaire-Chamley, M. / Issakidis-Bourguet, E. / Miginiac-Maslow, M. / Eklund, H.
History
DepositionFeb 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 4, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (MALATE DEHYDROGENASE)
B: PROTEIN (MALATE DEHYDROGENASE)
C: PROTEIN (MALATE DEHYDROGENASE)
D: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,57821
Polymers163,4664
Non-polymers1,11217
Water4,774265
1
A: PROTEIN (MALATE DEHYDROGENASE)
B: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,32211
Polymers81,7332
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-287 kcal/mol
Surface area27140 Å2
MethodPISA, PQS
2
C: PROTEIN (MALATE DEHYDROGENASE)
D: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,25610
Polymers81,7332
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-182 kcal/mol
Surface area26910 Å2
MethodPISA, PQS
3
A: PROTEIN (MALATE DEHYDROGENASE)
B: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules

A: PROTEIN (MALATE DEHYDROGENASE)
B: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,64322
Polymers163,4664
Non-polymers1,17718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11430 Å2
ΔGint-601 kcal/mol
Surface area53440 Å2
MethodPISA
4
C: PROTEIN (MALATE DEHYDROGENASE)
D: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules

C: PROTEIN (MALATE DEHYDROGENASE)
D: PROTEIN (MALATE DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,51220
Polymers163,4664
Non-polymers1,04716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area10770 Å2
ΔGint-385 kcal/mol
Surface area53110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.424, 153.944, 160.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.435112, 0.892298, -0.12034), (0.891967, -0.445405, -0.077517), (-0.122768, -0.073611, -0.989702)-15.34447, 46.59762, 158.62724
2given(0.07762, -0.996926, 0.010641), (0.99693, 0.077721, 0.009469), (-0.010267, 0.009874, 0.999899)-2.9889, 74.48865, 40.90058
3given(0.917302, -0.380449, -0.117537), (-0.390235, -0.91763, -0.075314), (-0.079202, 0.114952, -0.990209)41.79069, 94.4652, 199.81282

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Components

#1: Protein
PROTEIN (MALATE DEHYDROGENASE)


Mass: 40866.426 Da / Num. of mol.: 4 / Mutation: DELETION OF FIRST 15 N-TERMINAL RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Tissue: LEAF / Organelle: CHLOROPLAST / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17606, malate dehydrogenase (NADP+)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.74 Å3/Da / Density % sol: 61 % / Description: POLY-ALANINE MODEL
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.02 mMrecombinant E.coli11
210 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 66459 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.44 Å / % possible all: 99.8
Reflection
*PLUS
Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMD

1bmd


Resolution: 2.4→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 30748455.68 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2010 3 %RANDOM
Rwork0.221 ---
obs-66489 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---1.6 Å20 Å2
3---0.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10850 0 17 265 11132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.249
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.93
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: 2.4→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 119 3.5 %
Rwork0.245 3328 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.ZNTOPOLOGY.ZN
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor obs: 0.245

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