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- PDB-2hjr: Crystal Structure of Cryptosporidium parvum malate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2hjr
TitleCrystal Structure of Cryptosporidium parvum malate dehydrogenase
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / malaria / Cryptosporidium parvum / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


L-lactate dehydrogenase (NAD+) activity / lactate metabolic process
Similarity search - Function
Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / 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 ...Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / 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
ADENOSINE-5-DIPHOSPHORIBOSE / CITRIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWernimont, A.K. / Dong, A. / Lew, J. / Hassani, A. / Ren, H. / Qiu, W. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. ...Wernimont, A.K. / Dong, A. / Lew, J. / Hassani, A. / Ren, H. / Qiu, W. / Kozieradzki, I. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2007
Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.
Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
I: Malate dehydrogenase
J: Malate dehydrogenase
K: Malate dehydrogenase
L: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,38136
Polymers421,36412
Non-polymers9,01724
Water24,0861337
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-34 kcal/mol
Surface area25090 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area25150 Å2
MethodPISA
3
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-31 kcal/mol
Surface area25020 Å2
MethodPISA
4
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-34 kcal/mol
Surface area25280 Å2
MethodPISA
5
I: Malate dehydrogenase
J: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-33 kcal/mol
Surface area25130 Å2
MethodPISA
6
K: Malate dehydrogenase
L: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-36 kcal/mol
Surface area25120 Å2
MethodPISA
7
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,46012
Polymers140,4554
Non-polymers3,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20020 Å2
ΔGint-129 kcal/mol
Surface area41070 Å2
MethodPISA
8
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,46012
Polymers140,4554
Non-polymers3,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20010 Å2
ΔGint-131 kcal/mol
Surface area40990 Å2
MethodPISA
9
I: Malate dehydrogenase
J: Malate dehydrogenase
K: Malate dehydrogenase
L: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,46012
Polymers140,4554
Non-polymers3,0068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20040 Å2
ΔGint-133 kcal/mol
Surface area41060 Å2
MethodPISA
10
I: Malate dehydrogenase
L: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-58 kcal/mol
Surface area23740 Å2
MethodPISA
11
F: Malate dehydrogenase
H: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-56 kcal/mol
Surface area23870 Å2
MethodPISA
12
B: Malate dehydrogenase
C: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-57 kcal/mol
Surface area23570 Å2
MethodPISA
13
E: Malate dehydrogenase
G: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-50 kcal/mol
Surface area23650 Å2
MethodPISA
14
J: Malate dehydrogenase
K: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-54 kcal/mol
Surface area23780 Å2
MethodPISA
15
A: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7306
Polymers70,2272
Non-polymers1,5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-50 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.887, 171.887, 135.606
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 13 - 324 / Label seq-ID: 13 - 324

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
DetailsBiological assembly is a dimer, can be made of monomers A and B

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Components

#1: Protein
Malate dehydrogenase


Mass: 35113.645 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: adjacent gene encodes predicted lactate dehydrogenase
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CYZ3
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1337 / Source method: isolated from a natural source / Formula: H2O

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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: 55.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG4K, 0.2M NH4oAC, Nacitrate pH 5.6, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 227472 / Num. obs: 227351 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.117 / Rsym value: 0.075 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.911 / Num. unique all: 22734 / Rsym value: 0.737 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUY

1guy


Resolution: 2.2→19.83 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.099 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24747 11391 5 %RANDOM
Rwork0.19799 ---
all0.20048 ---
obs0.20048 215627 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.344 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28040 0 588 1337 29965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02229018
X-RAY DIFFRACTIONr_angle_refined_deg1.5162.00439347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2953751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96525.931032
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.785155060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4291572
X-RAY DIFFRACTIONr_chiral_restr0.1250.24682
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220920
X-RAY DIFFRACTIONr_nbd_refined0.2140.214747
X-RAY DIFFRACTIONr_nbtor_refined0.30.220219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.21868
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.226
X-RAY DIFFRACTIONr_mcbond_it0.6281.519047
X-RAY DIFFRACTIONr_mcangle_it1.085229960
X-RAY DIFFRACTIONr_scbond_it1.817311096
X-RAY DIFFRACTIONr_scangle_it2.8394.59387
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1244medium positional0.190.5
2B1244medium positional0.170.5
3C1244medium positional0.160.5
4D1244medium positional0.190.5
5E1244medium positional0.150.5
6F1244medium positional0.220.5
7G1244medium positional0.220.5
8H1244medium positional0.230.5
9I1244medium positional0.190.5
10J1244medium positional0.180.5
11K1244medium positional0.260.5
12L1244medium positional0.170.5
1A1071loose positional0.575
2B1071loose positional0.535
3C1071loose positional0.565
4D1071loose positional0.455
5E1071loose positional0.475
6F1071loose positional0.565
7G1071loose positional0.475
8H1071loose positional0.555
9I1071loose positional0.475
10J1071loose positional0.475
11K1071loose positional0.55
12L1071loose positional0.585
1A1244medium thermal0.752
2B1244medium thermal1.072
3C1244medium thermal1.062
4D1244medium thermal0.632
5E1244medium thermal0.972
6F1244medium thermal1.032
7G1244medium thermal0.92
8H1244medium thermal0.832
9I1244medium thermal0.842
10J1244medium thermal1.262
11K1244medium thermal0.962
12L1244medium thermal0.872
1A1071loose thermal1.5410
2B1071loose thermal1.9610
3C1071loose thermal2.0210
4D1071loose thermal1.5310
5E1071loose thermal1.8210
6F1071loose thermal1.9210
7G1071loose thermal1.9410
8H1071loose thermal1.7510
9I1071loose thermal1.6710
10J1071loose thermal2.110
11K1071loose thermal2.0210
12L1071loose thermal1.8210
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 861 -
Rwork0.258 15821 -
obs--99.87 %

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