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- PDB-6dnt: UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter rumin... -

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Basic information

Entry
Database: PDB / ID: 6dnt
TitleUDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with UDP-N-acetylmuramic acid
ComponentsNAD-dependent epimerase/dehydratase
KeywordsSUGAR BINDING PROTEIN / UDP-N-acetylglucosamine / WbpP / 4-epimerase / UDP-N-acetylmuramic acid
Function / homology
Function and homology information


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
Chem-EPZ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesMethanobrevibacter ruminantium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsCarbone, V. / Schofield, L.R. / Sang, C. / Sutherland-Smith, A.J. / Ronimus, R.S.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Royal Society of New ZealandAGR1301 New Zealand
Pastoral Greenhouse Gas Research Consortium (PGgRc) New Zealand
CitationJournal: Proteins / Year: 2018
Title: Structural determination of archaeal UDP-N-acetylglucosamine 4-epimerase from Methanobrevibacter ruminantium M1 in complex with the bacterial cell wall intermediate UDP-N-acetylmuramic acid.
Authors: Carbone, V. / Schofield, L.R. / Sang, C. / Sutherland-Smith, A.J. / Ronimus, R.S.
History
DepositionJun 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2928
Polymers38,6361
Non-polymers1,6577
Water5,423301
1
A: NAD-dependent epimerase/dehydratase
hetero molecules

A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58416
Polymers77,2712
Non-polymers3,31314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area6120 Å2
ΔGint-17 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.497, 89.497, 82.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-403-

ZN

21A-793-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent epimerase/dehydratase


Mass: 38635.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1) (archaea)
Strain: ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1 / Gene: mru_1413 / Production host: Escherichia coli (E. coli) / References: UniProt: D3E402

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Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-EPZ / (2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid


Mass: 679.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N3O19P2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 5.9 and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→41.36 Å / Num. obs: 45299 / % possible obs: 97.8 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.026 / Rrim(I) all: 0.095 / Net I/σ(I): 22.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.773 / Num. unique obs: 1292 / CC1/2: 0.736 / Rpim(I) all: 0.248 / Rrim(I) all: 0.815 / % possible all: 56.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.338
Highest resolutionLowest resolution
Rotation39.36 Å2.5 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.28data scaling
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RU7

3ru7


Resolution: 1.66→41.36 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.509 / SU ML: 0.051 / SU R Cruickshank DPI: 0.0792 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.076
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1717 2149 4.7 %RANDOM
Rwork0.1518 ---
obs0.1527 43115 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.4 Å2 / Biso mean: 17.648 Å2 / Biso min: 8.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.66→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 109 301 2852
Biso mean--17.81 30.8 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192735
X-RAY DIFFRACTIONr_bond_other_d0.0020.022570
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9893725
X-RAY DIFFRACTIONr_angle_other_deg0.8952.9825965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57226.098123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17215475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.143157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023105
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02589
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 128 -
Rwork0.219 2868 -
all-2996 -
obs--90.13 %

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