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- PDB-2hrz: The crystal structure of the nucleoside-diphosphate-sugar epimera... -

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Basic information

Entry
Database: PDB / ID: 2hrz
TitleThe crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens
ComponentsNucleoside-diphosphate-sugar epimerase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nucleoside-diphosphate-sugar epimerase / Agrobacterium tumefaciens / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / 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
Nucleoside-diphosphate-sugar epimerase / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the nucleoside-diphosphate-sugar epimerase from Agrobacterium tumefaciens
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside-diphosphate-sugar epimerase


Theoretical massNumber of molelcules
Total (without water)37,5631
Polymers37,5631
Non-polymers00
Water5,693316
1
A: Nucleoside-diphosphate-sugar epimerase

A: Nucleoside-diphosphate-sugar epimerase


Theoretical massNumber of molelcules
Total (without water)75,1262
Polymers75,1262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Unit cell
Length a, b, c (Å)112.893, 112.893, 52.765
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Nucleoside-diphosphate-sugar epimerase / AGR_C_4963p


Mass: 37562.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: AGR_C_4963, Atu2738 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UBW2, UniProt: A9CHF5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 3.5M Na Formate, 0.1M MES6.0, 20% PEG10K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.85→97.59 Å / Num. all: 31621 / Num. obs: 31491 / % possible obs: 99.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 32.98
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.53 / Num. unique all: 2313 / % possible all: 99.75

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.006 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.134 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22457 1677 5.1 %RANDOM
Rwork0.18455 ---
all0.18647 31621 --
obs0.18647 31491 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.539 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.129 Å0.052 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.85→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 0 316 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222681
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.973625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35722.735117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62415444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0171524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022058
X-RAY DIFFRACTIONr_nbd_refined0.1970.21252
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.244
X-RAY DIFFRACTIONr_mcbond_it0.8621.51746
X-RAY DIFFRACTIONr_mcangle_it1.22522716
X-RAY DIFFRACTIONr_scbond_it2.31931038
X-RAY DIFFRACTIONr_scangle_it3.6634.5909
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 134 -
Rwork0.236 2307 -
obs-2307 99.75 %
Refinement TLS params.Method: refined / Origin x: 23.876 Å / Origin y: 77.065 Å / Origin z: 6.692 Å
111213212223313233
T0.0262 Å2-0.0069 Å20.0317 Å2--0.0159 Å2-0.0069 Å2---0.0477 Å2
L0.2915 °20.048 °20.0762 °2-0.304 °20.0045 °2--0.277 °2
S0.0048 Å °-0.0119 Å °-0.0233 Å °0.0242 Å °0.0002 Å °0.0467 Å °-0.0338 Å °-0.0319 Å °-0.0051 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-5 - 501 - 56
2X-RAY DIFFRACTION1AA51 - 10057 - 106
3X-RAY DIFFRACTION1AA101 - 150107 - 156
4X-RAY DIFFRACTION1AA151 - 200157 - 206
5X-RAY DIFFRACTION1AA201 - 250207 - 256
6X-RAY DIFFRACTION1AA251 - 300257 - 306
7X-RAY DIFFRACTION1AA301 - 336307 - 342

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