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- PDB-3dxf: Crystal structure of the HSCARG R37A mutant -

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Basic information

Entry
Database: PDB / ID: 3dxf
TitleCrystal structure of the HSCARG R37A mutant
ComponentsNmrA-like family domain-containing protein 1
KeywordsNADPH-BINDING PROTEIN / Rossmann fold
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionJul 24, 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 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 1.3Nov 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)66,6072
Polymers66,6072
Non-polymers00
Water00
1
A: NmrA-like family domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)33,3031
Polymers33,3031
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)33,3031
Polymers33,3031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.450, 88.090, 80.201
Angle α, β, γ (deg.)90.00, 89.69, 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 protein


Mass: 33303.258 Da / Num. of mol.: 2 / Mutation: R37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.96M ammonium sulfate, 0.1M sodium Hepes pH 7.2, 2% MPD, 20mM potassium chloride, 5mM Phenol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97928 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.2→26.7 Å / Num. obs: 32788 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 6.9 / Num. unique all: 24658 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EXX

2exx


Resolution: 2.2→26 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.833 / SU B: 7.102 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 1605 4.9 %RANDOM
Rwork0.24175 ---
obs0.24373 31182 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.598 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å20 Å2
2---0.26 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 0 0 4484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224555
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0871.9856148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3524.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8191531
X-RAY DIFFRACTIONr_chiral_restr0.070.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023406
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.22152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23068
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.2108
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.52929
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69724548
X-RAY DIFFRACTIONr_scbond_it0.9731815
X-RAY DIFFRACTIONr_scangle_it1.5384.51600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 122 -
Rwork0.246 2256 -
obs--99.62 %

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