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- PDB-3prj: Role of Packing Defects in the Evolution of Allostery and Induced... -

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Basic information

Entry
Database: PDB / ID: 3prj
TitleRole of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase.
ComponentsUDP-glucose 6-dehydrogenase
KeywordsOXIDOREDUCTASE / feedback inhibition / Rossmann fold / nucleotide sugar dehydrogenase / NAD binding / cytosol
Function / homology
Function and homology information


Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development / NAD binding / carbohydrate metabolic process / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain ...UDP-glucose 6-dehydrogenase, eukaryotic type / UDP-glucose/GDP-mannose dehydrogenase, N-terminal / UDP-glucose/GDP-mannose dehydrogenase, dimerisation / UDP-glucose/GDP-mannose dehydrogenase, C-terminal / UDP-glucose/GDP-mannose dehydrogenase / UDP-glucose/GDP-mannose dehydrogenase, C-terminal domain superfamily / UDP-glucose/GDP-mannose dehydrogenase family, central domain / UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain / UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain / UDP binding domain / Cytochrome c1, transmembrane anchor, C-terminal / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsKadirvelraj, R. / Wood, Z.A.
CitationJournal: Biochemistry / Year: 2011
Title: Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human UDP-Glucose Dehydrogenase.
Authors: Kadirvelraj, R. / Sennett, N.C. / Polizzi, S.J. / Weitzel, S. / Wood, Z.A.
History
DepositionNov 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 21, 2024Group: 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 / 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: UDP-glucose 6-dehydrogenase
B: UDP-glucose 6-dehydrogenase
C: UDP-glucose 6-dehydrogenase
D: UDP-glucose 6-dehydrogenase
E: UDP-glucose 6-dehydrogenase
F: UDP-glucose 6-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,77418
Polymers330,5646
Non-polymers7,21012
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34940 Å2
ΔGint-235 kcal/mol
Surface area97460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.790, 160.640, 205.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 3 / Auth seq-ID: 2 - 462 / Label seq-ID: 2 - 462

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
UDP-glucose 6-dehydrogenase / / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH


Mass: 55093.938 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 pLysS / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE


Mass: 536.276 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H22N2O16P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG3350, 0.9 M hexanediol, 0.1 M HEPES pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR 300 / Detector: CCD / Date: Nov 25, 2008
RadiationMonochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.3 Å / Num. obs: 65825 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 48.517 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.1-3.180.3633.8159584582192.5
3.18-3.270.2974.8172904700197.1
3.27-3.360.2515.9172764571197.6
3.36-3.470.1967.2169864458197.2
3.47-3.580.1578.9170814355197.8
3.58-3.710.12211.5163214109195.9
3.71-3.850.10313.5168454092198
3.85-40.09314.9162043894197.4
4-4.180.07717.8159043753198
4.18-4.380.06121.1153603593197.8
4.38-4.620.05424146943438198.2
4.62-4.90.05124.7139773278197.7
4.9-5.240.05224.9131523047198
5.24-5.660.05424124912863197.8
5.66-6.20.05523.7115572656197.9
6.2-6.930.04925.9103762397197.6
6.93-80.03333.990832104196.5
8-9.80.02642.774261792195.6
9.8-13.860.0244557671403195.3
13.86-48.30.02543.22847740185.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.13 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.27 Å47 Å
Translation3.27 Å47 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345300data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.29 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2372 / WRfactor Rwork: 0.1985 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7989 / SU B: 23.471 / SU ML: 0.392 / SU Rfree: 0.518 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 3314 5 %RANDOM
Rwork0.2279 ---
obs0.2301 65825 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.03 Å2 / Biso mean: 54.4558 Å2 / Biso min: 3.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.518 Å0.392 Å
Refinement stepCycle: LAST / Resolution: 3.1→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21569 0 468 148 22185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02222485
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.98930508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24652741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64724.303990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.809153929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.08115150
X-RAY DIFFRACTIONr_chiral_restr0.0930.23514
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116602
X-RAY DIFFRACTIONr_mcbond_it0.4691.513697
X-RAY DIFFRACTIONr_mcangle_it0.933222193
X-RAY DIFFRACTIONr_scbond_it1.30938788
X-RAY DIFFRACTIONr_scangle_it2.4524.58315
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1816TIGHT POSITIONAL0.060.05
2B1816TIGHT POSITIONAL0.050.05
3C1816TIGHT POSITIONAL0.050.05
4D1816TIGHT POSITIONAL0.040.05
5E1816TIGHT POSITIONAL0.050.05
6F1816TIGHT POSITIONAL0.050.05
1A1747LOOSE POSITIONAL0.065
2B1747LOOSE POSITIONAL0.055
3C1747LOOSE POSITIONAL0.065
4D1747LOOSE POSITIONAL0.055
5E1747LOOSE POSITIONAL0.055
6F1747LOOSE POSITIONAL0.055
1A1816TIGHT THERMAL0.070.5
2B1816TIGHT THERMAL0.080.5
3C1816TIGHT THERMAL0.080.5
4D1816TIGHT THERMAL0.070.5
5E1816TIGHT THERMAL0.10.5
6F1816TIGHT THERMAL0.070.5
1A1747LOOSE THERMAL0.0910
2B1747LOOSE THERMAL0.0810
3C1747LOOSE THERMAL0.0910
4D1747LOOSE THERMAL0.0810
5E1747LOOSE THERMAL0.110
6F1747LOOSE THERMAL0.0810
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 221 -
Rwork0.34 4344 -
all-4565 -
obs-4582 92.47 %

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