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- PDB-3e5m: Crystal structure of the HSCARG Y81A mutant -

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Basic information

Entry
Database: PDB / ID: 3e5m
TitleCrystal structure of the HSCARG Y81A mutant
ComponentsNmrA-like family domain-containing protein 1
KeywordsOXIDOREDUCTASE / Rossmann fold / Polymorphism
Function / homology
Function and homology information


Urea cycle / perinuclear region of cytoplasm / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / 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
NmrA-like family domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, Y. / Meng, G. / Dai, X. / Luo, M. / Zheng, X.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: NADPH is an allosteric regulator of HSCARG
Authors: Dai, X. / Li, Y. / Meng, G. / Yao, S. / Zhao, Y. / Yu, Q. / Zhang, J. / Luo, M. / Zheng, X.
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NmrA-like family domain-containing protein 1
B: NmrA-like family domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)66,5952
Polymers66,5952
Non-polymers00
Water00
1
A: NmrA-like family domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)33,2971
Polymers33,2971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NmrA-like family domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)33,2971
Polymers33,2971
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.956, 89.036, 84.182
Angle α, β, γ (deg.)90.00, 88.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NmrA-like family domain-containing protein 1 / HSCARG


Mass: 33297.277 Da / Num. of mol.: 2 / Mutation: Y81A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMRAL1, HSCARG / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9HBL8

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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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 3% MPD, 10mM potassium chloride, 0.1M sodium Hepes, 1.86M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. obs: 22513 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EXX

2exx


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.79 / Cor.coef. Fo:Fc free: 0.75 / SU B: 14.63 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.794 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27267 892 4.8 %RANDOM
Rwork0.26022 ---
obs0.26081 17638 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.867 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å2-0.7 Å2
2--0.2 Å20 Å2
3---1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 0 0 4605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224710
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.986366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8115590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44723.905210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.57815836
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6351534
X-RAY DIFFRACTIONr_chiral_restr0.4550.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.22162
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.23086
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2810.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5231.53023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14424703
X-RAY DIFFRACTIONr_scbond_it2.7831840
X-RAY DIFFRACTIONr_scangle_it3.6674.51663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 59 -
Rwork0.283 1207 -
obs-993 91.47 %

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