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- PDB-4a7p: Se-Met derivatized UgdG, UDP-glucose dehydrogenase from Sphingomo... -

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Basic information

Entry
Database: PDB / ID: 4a7p
TitleSe-Met derivatized UgdG, UDP-glucose dehydrogenase from Sphingomonas elodea
ComponentsUDP-GLUCOSE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CARBOHYDRATE SYNTHESIS / EXOPOLYSACCHARIDE / GELLAN
Function / homology
Function and homology information


UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding
Similarity search - Function
UDP-glucose 6-dehydrogenase, bacterial 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, bacterial 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 6-dehydrogenase
Similarity search - Component
Biological speciesSPHINGOMONAS ELODEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.403 Å
AuthorsRocha, J. / Granja, A.T. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.
Citation
Journal: To be Published
Title: The Structure of Ugdg, an Udp-Glucose Dehydrogenase from Sphingomonas Elodea Atcc 31461
Authors: Rocha, J. / Granja, A.T. / Sa-Correia, I. / Fialho, A.M. / Frazao, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Cloning, Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Ugdg, an Udp-Glucose Dehydrogenase from Sphingomonas Elodea Atcc 31461.
Authors: Rocha, J. / Granja, A.T. / Sa-Correia, I. / Fialho, A. / Frazao, C.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.4Nov 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 DEHYDROGENASE
B: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2264
Polymers96,8992
Non-polymers1,3272
Water00
1
A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules

A: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2264
Polymers96,8992
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area7520 Å2
ΔGint-58.3 kcal/mol
Surface area33430 Å2
MethodPISA
2
B: UDP-GLUCOSE DEHYDROGENASE
hetero molecules

B: UDP-GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2264
Polymers96,8992
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_667-y+1,-x+1,-z+5/21
Buried area7540 Å2
ΔGint-56.6 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.030, 109.030, 175.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:189 OR RESSEQ 195:248 OR RESSEQ 253:435 OR RESSEQ 501:501 )
211CHAIN B AND (RESSEQ 1:189 OR RESSEQ 195:248 OR RESSEQ 253:435 OR RESSEQ 501:501 )

NCS oper: (Code: given
Matrix: (-0.22146, 0.776726, 0.58962), (0.792343, -0.20914, 0.573108), (0.568461, 0.594102, -0.569118)
Vector: -203.418, -5.15969, 280.045)

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Components

#1: Protein UDP-GLUCOSE DEHYDROGENASE / UGDG SE-MET FORM


Mass: 48449.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SE-METHIONINE DERIVATIZED UGDG / Source: (gene. exp.) SPHINGOMONAS ELODEA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / References: UniProt: A4UTT2, UDP-glucose 6-dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
Has protein modificationY
Sequence detailsCRYSTALLIZED PROTEIN CONTAINS ADDITIONAL N-TERMINAL HISTIDINE TAG AND LINKER HHHHHHGS. ...CRYSTALLIZED PROTEIN CONTAINS ADDITIONAL N-TERMINAL HISTIDINE TAG AND LINKER HHHHHHGS. ADDITIONALLY, ALL METHIONINE RESIDUES WERE DERIVATISED INTO SELENO- METHIONINE RESIDUES. THIS SE-MET UGDG PROTEIN STRUCTURE CORRESPONDS TO THE SE-MET DERIVATIZED DNA SEQUENCE OF GENBANK ENTRY EF488145.2, WHERE UGDG CORRESPONDS TO NUCLEOTIDES 1359-2675. UGDG THUS BEGINS WITH NUCLEOTIDES 1359-13560-13561, WHICH FORM THE CODON GTG. THE CANONICAL TRANSLATION OF CODON GTG IS VALINE, AS IN THE PRESENT STRUCTURE.ODDLY, IN ITS GENBANK ENTRY THE GTG FIRST CODON OF UGDG WAS WRONGLY TRANSLATED INTO METHIONINE.

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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: 2.65 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1 ML DROPS OF PROTEIN SOLUTION, 5.5 MG/ML SE-MET UGDG IN 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT AND 1 MM NAD, WERE MIXED WITH 1 ML DROPS OF PRECIPITANT SOLUTION, 0.1 M MES PH 6.5, 40 ...Details: 1 ML DROPS OF PROTEIN SOLUTION, 5.5 MG/ML SE-MET UGDG IN 25 MM TRIS-HCL PH 8.3, 50 MM NACL, 2.5 MM DTT AND 1 MM NAD, WERE MIXED WITH 1 ML DROPS OF PRECIPITANT SOLUTION, 0.1 M MES PH 6.5, 40 % (W/V) PEG 200, AND LET EQUILIBRATE BY VAPOR DIFFUSION AGAINST 500 ML PRECIPITANT SOLUTION AT 293 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 2, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.4→48.78 Å / Num. obs: 27657 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 121.79 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.1
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

Software
NameClassification
FFFEARmodel building
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
RESOLVEphasing
FFFEARphasing
XFITphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.403→48.76 Å / SU ML: 0.91 / σ(F): 1.38 / Phase error: 21.28 / Stereochemistry target values: ML
Details: SE-MET UGDG SAD PHASES LED TO A PRELIMINARY MODEL, WITH 346 OUT OF 438 RESIDUES OF WHICH 318 WERE ASSIGNED AS ALANINES, WHICH WAS USED FOR MOLECULAR REPLACEMENT OF A NATIVE UGDG HEXAGONAL ...Details: SE-MET UGDG SAD PHASES LED TO A PRELIMINARY MODEL, WITH 346 OUT OF 438 RESIDUES OF WHICH 318 WERE ASSIGNED AS ALANINES, WHICH WAS USED FOR MOLECULAR REPLACEMENT OF A NATIVE UGDG HEXAGONAL CRYSTAL THAT DIFFRACTED UP TO 2.15 ANGSTROM RESOLUTION. THE REFINED NATIVE UGDG HEXAGONAL MODEL WAS THEN USED WITH THE PRESENT SE-MET UGDG DATA TO REFINE THE HERE PRESENTED SE-MET UGDG STRUCTURE. THE SE-MET UGDG REFINEMENT CONVERGED TO R-WORK AND R-FREE OF 0.2018 AND 0.2342, RESPECTIVELY, USING A THIN-SHELLS R-FREE SET WITH 1859 REFLECTIONS. THE FINAL SE-MET UGDG MODEL WAS THEN REFINED WEIGHTING THE STEREO-CHEMICAL AND ADP RESTRAINTS VERSUS THE FULL DATA SET IN ORDER TO OBTAIN BOND DISTANCES, ANGLES AND ADP RMSDS SIMILAR TO THOSE OBTAINED IN THE PRECEDENT R-FREE GUIDED REFINEMENT.
RfactorNum. reflection% reflection
Rwork0.2298 --
obs-27657 99.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.669 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 130 Å2
Baniso -1Baniso -2Baniso -3
1--10.0266 Å20 Å20 Å2
2---10.0266 Å20 Å2
3---20.0532 Å2
Refinement stepCycle: LAST / Resolution: 3.403→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 88 0 6557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046665
X-RAY DIFFRACTIONf_angle_d1.0119047
X-RAY DIFFRACTIONf_dihedral_angle_d17.8352456
X-RAY DIFFRACTIONf_chiral_restr0.0681055
X-RAY DIFFRACTIONf_plane_restr0.0051177
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3260X-RAY DIFFRACTIONPOSITIONAL
12B3260X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.403-3.44170.29459190.2945919X-RAY DIFFRACTION99
3.4417-3.48220.30499070.3049907X-RAY DIFFRACTION100
3.4822-3.52460.3129290.312929X-RAY DIFFRACTION100
3.5246-3.56920.2739180.273918X-RAY DIFFRACTION100
3.5692-3.61620.28279330.2827933X-RAY DIFFRACTION100
3.6162-3.66570.27169240.2716924X-RAY DIFFRACTION100
3.6657-3.71810.24059160.2405916X-RAY DIFFRACTION100
3.7181-3.77350.25779410.2577941X-RAY DIFFRACTION100
3.7735-3.83250.26319370.2631937X-RAY DIFFRACTION100
3.8325-3.89530.24239390.2423939X-RAY DIFFRACTION100
3.8953-3.96240.26078970.2607897X-RAY DIFFRACTION100
3.9624-4.03450.24799480.2479948X-RAY DIFFRACTION100
4.0345-4.1120.23218990.2321899X-RAY DIFFRACTION100
4.112-4.19590.22769250.2276925X-RAY DIFFRACTION100
4.1959-4.28710.22019200.2201920X-RAY DIFFRACTION100
4.2871-4.38670.20399270.2039927X-RAY DIFFRACTION100
4.3867-4.49640.23429240.2342924X-RAY DIFFRACTION100
4.4964-4.61790.21079230.2107923X-RAY DIFFRACTION100
4.6179-4.75360.21939290.2193929X-RAY DIFFRACTION100
4.7536-4.90690.23279210.2327921X-RAY DIFFRACTION100
4.9069-5.08210.23529230.2352923X-RAY DIFFRACTION100
5.0821-5.28540.22519250.2251925X-RAY DIFFRACTION100
5.2854-5.52560.25339300.2533930X-RAY DIFFRACTION100
5.5256-5.81650.25229260.2522926X-RAY DIFFRACTION100
5.8165-6.18020.26889150.2688915X-RAY DIFFRACTION100
6.1802-6.65630.23919390.2391939X-RAY DIFFRACTION100
6.6563-7.32420.25289230.2528923X-RAY DIFFRACTION100
7.3242-8.37940.19779240.1977924X-RAY DIFFRACTION100
8.3794-10.53950.15718970.1571897X-RAY DIFFRACTION98
10.5395-48.76470.22638790.2263879X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6901-1.9883-0.84261.75980.72352.5264-0.17080.6019-0.754-0.0284-0.56820.95860.1295-1.1041-0.340.7764-0.23810.30370.8239-0.19821.13782.584765.618220.2009
20.82110.73560.7561.4418-0.69493.149-0.54460.34390.012-0.7531-0.1885-0.8763-0.11181.8975-0.13820.63190.072-0.02371.137-0.05370.747921.983192.8907211.9689
31.72580.10890.79082.1352-0.04151.59430.00860.9739-0.1905-0.7719-0.05720.1353-0.0890.03470.02860.7518-0.0293-0.03010.9239-0.20160.469310.026988.9554197.9496
42.31940.2988-0.59331.61440.72322.3929-0.7389-0.28370.1716-0.0115-0.02580.3510.15040.0278-1.76120.7413-0.081-0.36930.7028-0.250.7591-23.5351109.7471196.224
54.9522-1.1314.45446.4105-1.1694.00650.2533-1.6839-0.0471.65670.27730.8142-0.178-0.99150.59760.4269-0.03350.10990.6344-0.3950.7228-10.8946113.9094227.9439
61.04080.2090.68321.3678-0.70062.0867-0.0221-0.33410.10350.148-0.27611.0571-0.2578-0.7249-0.30840.4219-0.10420.09020.6873-0.19840.744-19.366197.3094226.5143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -1:209)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 210:253)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 254:438)
4X-RAY DIFFRACTION4(CHAIN B AND RESID -1:209)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 210:253)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 254:438)

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