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- PDB-6mnz: Crystal structure of RibBX, a two domain 3,4-dihydroxy-2-butanone... -

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Basic information

Entry
Database: PDB / ID: 6mnz
TitleCrystal structure of RibBX, a two domain 3,4-dihydroxy-2-butanone 4-phosphate synthase from A. baumannii.
Components3,4-dihydroxy-2-butanone 4-phosphate synthase
KeywordsLYASE / 3 / 4-dihydroxy-2-butanone 4-phosphate synthase
Function / homology
Function and homology information


3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / hydrolase activity / magnesium ion binding
Similarity search - Function
GTP cyclohydrolase II / GTP cyclohydrolase II superfamily / GTP cyclohydrolase II / 3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB / 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase RibB-like alpha/beta domain superfamily
Similarity search - Domain/homology
3,4-dihydroxy-2-butanone 4-phosphate synthase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.66 Å
AuthorsWang, J. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM118157 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: Multi-metal Restriction by Calprotectin Impacts De Novo Flavin Biosynthesis in Acinetobacter baumannii.
Authors: Wang, J. / Lonergan, Z.R. / Gonzalez-Gutierrez, G. / Nairn, B.L. / Maxwell, C.N. / Zhang, Y. / Andreini, C. / Karty, J.A. / Chazin, W.J. / Trinidad, J.C. / Skaar, E.P. / Giedroc, D.P.
History
DepositionOct 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3,4-dihydroxy-2-butanone 4-phosphate synthase
B: 3,4-dihydroxy-2-butanone 4-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,83913
Polymers81,9032
Non-polymers93511
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-150 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.707, 136.857, 51.856
Angle α, β, γ (deg.)90.000, 98.527, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYchain 'A'AA4 - 784 - 78
12GLYGLYALAALAchain 'A'AA82 - 27282 - 272
13VALVALALAALAchain 'A'AA289 - 304289 - 304
14ALAALAALAALAchain 'A'AA318 - 367318 - 367
21SERSERGLYGLYchain 'B'BB4 - 784 - 78
22GLYGLYALAALAchain 'B'BB82 - 27282 - 272
23VALVALALAALAchain 'B'BB289 - 304289 - 304
24ALAALAALAALAchain 'B'BB318 - 367318 - 367

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Components

#1: Protein 3,4-dihydroxy-2-butanone 4-phosphate synthase / DHBP synthase


Mass: 40951.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: ribB, ribBA, A7M79_16415, A7M90_07480, A7N09_07660, AB895_1395, APD06_16235, AZE33_19550, B4R90_18035, BGC29_12000, BWP00_07280, C2U32_13770, CAS83_08960, CBE85_14000, CHQ89_12900, CPI82_04655, ...Gene: ribB, ribBA, A7M79_16415, A7M90_07480, A7N09_07660, AB895_1395, APD06_16235, AZE33_19550, B4R90_18035, BGC29_12000, BWP00_07280, C2U32_13770, CAS83_08960, CBE85_14000, CHQ89_12900, CPI82_04655, IX87_13995, LV38_00273
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: V5V8R9, 3,4-dihydroxy-2-butanone-4-phosphate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM MES ph 6.5, 100 mM NaCl, 150 mM ammonia sulfate, 19% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.66→68.43 Å / Num. obs: 22952 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.23 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.079 / Rrim(I) all: 0.153 / Net I/σ(I): 7.4
Reflection shellResolution: 2.66→2.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1147 / CC1/2: 0.557 / Rpim(I) all: 0.672 / Rrim(I) all: 1.309 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.66→68.43 Å / SU ML: 0.5226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4881
RfactorNum. reflection% reflection
Rfree0.303 1177 5.13 %
Rwork0.2778 --
obs0.2791 22929 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.53 Å2
Refinement stepCycle: LAST / Resolution: 2.66→68.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 47 122 5339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00245286
X-RAY DIFFRACTIONf_angle_d0.53897160
X-RAY DIFFRACTIONf_chiral_restr0.0422826
X-RAY DIFFRACTIONf_plane_restr00
X-RAY DIFFRACTIONf_dihedral_angle_d0.71331232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.780.44861590.40372705X-RAY DIFFRACTION99.76
2.78-2.930.45031620.37712740X-RAY DIFFRACTION99.9
2.93-3.110.34331290.34062748X-RAY DIFFRACTION99.76
3.11-3.350.33221520.29252708X-RAY DIFFRACTION99.48
3.35-3.690.33061270.27892732X-RAY DIFFRACTION98.69
3.69-4.220.31550.25162658X-RAY DIFFRACTION98.01
4.22-5.320.23591430.23062713X-RAY DIFFRACTION97.77
5.32-68.450.25671500.26012748X-RAY DIFFRACTION98.84

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