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- PDB-5k8b: X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulo... -

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Basic information

Entry
Database: PDB / ID: 5k8b
TitleX-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate
Components8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
KeywordsTRANSFERASE / Transaminase / 8-amino-3 / 8-dideoxy-d-manno-octulosonic acid / deoxy sugar
Function / homology
Function and homology information


8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase / lipopolysaccharide biosynthetic process / polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PDG / 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHolden, H.M. / Thoden, J.B. / Zachman-Brockmeyer, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Authors: Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M.
History
DepositionMay 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
B: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
C: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
D: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,78614
Polymers179,0734
Non-polymers1,71310
Water12,791710
1
A: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
B: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3997
Polymers89,5372
Non-polymers8635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-90 kcal/mol
Surface area26630 Å2
MethodPISA
2
C: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
D: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3877
Polymers89,5372
Non-polymers8505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-87 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.628, 61.675, 99.636
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase


Mass: 44768.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: kdnA, SO_2476 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8EEB1, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase
#2: Chemical
ChemComp-PDG / N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID / N-PYRIDOXYL-D-GLUTAMIC ACID-5'-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H19N2O9P
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16-21% PEG-3350, 100 mM MES, 200 mM KCl, 150 mM MgCl2, 1 mM PLP, 50 mM monosodium glutamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 83041 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.4 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FRK

3frk


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.549 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22571 4100 4.9 %RANDOM
Rwork0.17144 ---
obs0.1742 78941 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.988 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0.81 Å2
2--2.69 Å20 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12192 0 106 710 13008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212004
X-RAY DIFFRACTIONr_angle_refined_deg2.1261.95816991
X-RAY DIFFRACTIONr_angle_other_deg1.183327710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9551580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49824.818548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.805152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8011556
X-RAY DIFFRACTIONr_chiral_restr0.1470.21872
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114206
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022770
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.012.1246308
X-RAY DIFFRACTIONr_mcbond_other2.012.1236307
X-RAY DIFFRACTIONr_mcangle_it3.0573.1767880
X-RAY DIFFRACTIONr_mcangle_other3.0573.1777881
X-RAY DIFFRACTIONr_scbond_it2.6392.4026263
X-RAY DIFFRACTIONr_scbond_other2.6392.4026259
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1073.4849102
X-RAY DIFFRACTIONr_long_range_B_refined5.30516.86314930
X-RAY DIFFRACTIONr_long_range_B_other5.26316.79914659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 261 -
Rwork0.253 5407 -
obs--88.29 %

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