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- PDB-3g79: Crystal structure of NDP-N-acetyl-D-galactosaminuronic acid dehyd... -

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Basic information

Entry
Database: PDB / ID: 3g79
TitleCrystal structure of NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase from Methanosarcina mazei Go1
ComponentsNDP-N-acetyl-D-galactosaminuronic acid dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase / PSI-2 / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


UDP-N-acetyl-D-mannosamine dehydrogenase / UDP-N-acetyl-D-mannosamine dehydrogenase activity / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / polysaccharide biosynthetic process / NAD binding / membrane => GO:0016020
Similarity search - Function
UDP-N-acetyl-D-mannosamine/glucosamine dehydrogenase / 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-N-acetyl-D-mannosamine/glucosamine dehydrogenase / 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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-ManNAc 6-dehydrogenase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase from Methanosarcina mazei Go1
Authors: Malashkevich, V.N. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase
B: NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase


Theoretical massNumber of molelcules
Total (without water)103,9672
Polymers103,9672
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-48.4 kcal/mol
Surface area38490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.830, 88.723, 151.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 1 / Auth seq-ID: -999 - 999 / Label seq-ID: -999 - 999

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein NDP-N-acetyl-D-galactosaminuronic acid dehydrogenase


Mass: 51983.566 Da / Num. of mol.: 2 / Fragment: UNP residues 3-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei Go1 (archaea) / Strain: Go1 / DSM 3647 / Goe1 / JCM 11883 / OCM 88 / Gene: MM_1154 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q8PXR2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 3000, 0.1M Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2008
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 86212 / % possible obs: 99.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.133 / Χ2: 7.709 / Net I/σ(I): 32.808
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.219 / Num. unique all: 2060 / Χ2: 2.147 / % possible all: 99.6

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Phasing

Phasing dmFOM : 0.72 / FOM acentric: 0.73 / FOM centric: 0.62 / Reflection: 21241 / Reflection acentric: 18731 / Reflection centric: 2510
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-34.440.890.920.82987705282
5.4-8.60.830.860.6729522447505
4.3-5.40.820.840.6936253170455
3.8-4.30.790.80.6935873202385
3.2-3.80.670.680.5263285743585
3-3.20.50.510.3937623464298

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.291 / WRfactor Rwork: 0.219 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.762 / SU B: 23.706 / SU ML: 0.251 / SU R Cruickshank DPI: 0.518 / SU Rfree: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.516 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. 3. The Friedel pairs were used in phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2038 5.1 %RANDOM
Rwork0.222 ---
obs0.225 40272 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 94.42 Å2 / Biso mean: 37.458 Å2 / Biso min: 9.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7242 0 0 179 7421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227406
X-RAY DIFFRACTIONr_angle_refined_deg1.891.97510010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3355950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85924.183306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.884151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9461544
X-RAY DIFFRACTIONr_chiral_restr0.140.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215542
X-RAY DIFFRACTIONr_mcbond_it1.1343.54710
X-RAY DIFFRACTIONr_mcangle_it4.753507556
X-RAY DIFFRACTIONr_scbond_it11.746502696
X-RAY DIFFRACTIONr_scangle_it1.0434.52454
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3633 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.825
BTIGHT THERMAL3.4110
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 146 -
Rwork0.29 2843 -
all-2989 -
obs--97.74 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2571-0.0443-0.16250.85960.2430.76930.01370.06890.07910.0205-0.02470.0467-0.11430.04810.01090.0242-0.0159-0.0160.03450.03620.102510.0963-5.156-2.8526
20.4720.35270.31320.54910.30660.70730.0344-0.0311-0.08280.0586-0.0667-0.00110.11690.05590.03230.02230.00770.00590.02430.01410.08799.9315-42.2439-0.7879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 478
2X-RAY DIFFRACTION2A4 - 478

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