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- PDB-6xig: X-ray crystal structure of MqnE from Pedobacter heparinus -

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Basic information

Entry
Database: PDB / ID: 6xig
TitleX-ray crystal structure of MqnE from Pedobacter heparinus
ComponentsAminodeoxyfutalosine synthase
KeywordsBIOSYNTHETIC PROTEIN / Iron-Sulfur cluster / Radical SAM / menaquinone biosynthesis
Function / homology
Function and homology information


aminodeoxyfutalosine synthase / aminodeoxyfutalosine synthase activity / menaquinone biosynthetic process / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
FO synthase, subunit 2 / Aminodeoxyfutalosine synthase / F420, menaquinone cofactor biosynthesis / CofH/MqnC-like, C-terminal domain / CofH/MqnC C-terminal region / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / D(-)-TARTARIC ACID / Aminodeoxyfutalosine synthase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsGrove, T.L. / Bonanno, J.B. / Almo, S.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI133329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118303-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM093342 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094662 United States
CitationJournal: Biochemistry / Year: 2020
Title: Narrow-Spectrum Antibiotic Targeting of the Radical SAM Enzyme MqnE in Menaquinone Biosynthesis.
Authors: Carl, A.G. / Harris, L.D. / Feng, M. / Nordstrom, L.U. / Gerfen, G.J. / Evans, G.B. / Silakov, A. / Almo, S.C. / Grove, T.L.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Mar 6, 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

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Assembly

Deposited unit
A: Aminodeoxyfutalosine synthase
B: Aminodeoxyfutalosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2049
Polymers97,7512
Non-polymers1,4547
Water16,195899
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-53 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.968, 75.403, 83.921
Angle α, β, γ (deg.)90.000, 107.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminodeoxyfutalosine synthase / Aminofutalosine synthase / Menaquinone biosynthetic enzyme MqnE


Mass: 48875.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3) (bacteria)
Strain: ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3
Gene: mqnE, Phep_1880
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C6XW09, aminodeoxyfutalosine synthase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 899 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K-Na-Tartrate, 20% polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98393 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98393 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 216048 / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Χ2: 0.934 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.633.40.614109900.6850.3870.7290.65497.4
1.63-1.663.40.524110860.7530.330.6220.65298
1.66-1.693.40.454111700.7940.2870.5390.67798.3
1.69-1.723.40.408110820.8330.2590.4850.69598.5
1.72-1.763.40.358111700.8580.2290.4270.71298.5
1.76-1.83.40.3110690.8960.1920.3580.7298.2
1.8-1.853.30.257111090.9170.1670.3080.75697.9
1.85-1.93.20.239109460.940.1570.2870.81996.9
1.9-1.953.20.213110120.9160.1410.2571.42897.2
1.95-2.023.10.148108780.9690.0990.1790.90196.3
2.02-2.092.80.11198370.9760.080.1370.94387.1
2.09-2.1730.094103900.9850.0640.1140.96491.9
2.17-2.273.20.104106640.980.0670.1251.57694.3
2.27-2.393.30.074106770.9920.0470.0880.99294.6
2.39-2.543.50.063110880.9940.0390.0741.01698.1
2.54-2.733.50.052110460.9960.0330.0611.06698
2.73-3.013.40.042112020.9970.0270.051.08898.5
3.01-3.443.20.032108850.9980.0210.0391.09496.4
3.44-4.332.70.02684570.9980.0180.0311.14474.9
4.33-203.80.025112900.9990.0150.0290.99699.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.59→19.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.655 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 5639 5.1 %RANDOM
Rwork0.1559 ---
obs0.1572 105344 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.57 Å2 / Biso mean: 18.357 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.78 Å2
2---0.07 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.59→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6249 0 66 899 7214
Biso mean--33.28 28.82 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175885
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.6638874
X-RAY DIFFRACTIONr_angle_other_deg1.8691.58613681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4755777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4222.617386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.153151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9451541
X-RAY DIFFRACTIONr_chiral_restr0.10.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021417
LS refinement shellResolution: 1.595→1.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 374 -
Rwork0.221 7501 -
all-7875 -
obs--92.51 %

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