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- PDB-6xi9: X-ray crystal structure of MqnE from Pedobacter heparinus in comp... -

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Basic information

Entry
Database: PDB / ID: 6xi9
TitleX-ray crystal structure of MqnE from Pedobacter heparinus in complex with aminofutalosine and methionine
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
METHIONINE / IRON/SULFUR CLUSTER / Chem-V47 / Aminodeoxyfutalosine synthase
Similarity search - Component
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 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)99,6149
Polymers97,7512
Non-polymers1,8647
Water10,413578
1
A: Aminodeoxyfutalosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8255
Polymers48,8751
Non-polymers9504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminodeoxyfutalosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7894
Polymers48,8751
Non-polymers9143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.512, 75.079, 83.269
Angle α, β, γ (deg.)90.000, 107.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 585 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-V47 / 9-[7-(3-carboxyphenyl)-5,6-dideoxy-beta-D-ribo-heptodialdo-1,4-furanosyl]-9H-purin-6-amine / Aminofutalosine


Mass: 413.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19N5O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 298 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: 2.14→20 Å / Num. obs: 46050 / % possible obs: 97.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.05 / Rrim(I) all: 0.126 / Χ2: 0.387 / Net I/σ(I): 4.6 / Num. measured all: 280095
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.185.90.60923160.7910.2720.670.26698.7
2.18-2.225.80.56523120.80.2530.6210.27698
2.22-2.265.70.50723130.8270.2290.5580.3698.2
2.26-2.315.70.45823080.8810.2060.5040.28398.3
2.31-2.365.80.40123100.8980.180.4410.27197.8
2.36-2.415.60.36822840.9150.1680.4060.27997.5
2.41-2.475.30.33222700.9190.1570.3690.28296.4
2.47-2.5450.29320410.9270.1410.3270.2885.9
2.54-2.615.50.25522600.9540.1170.2820.28994.5
2.61-2.76.60.22123340.9750.0920.2390.31399.3
2.7-2.796.70.1923430.9810.0790.2060.30799.4
2.79-2.96.80.16623720.9870.0680.180.3299.6
2.9-3.036.90.13523350.9920.0550.1460.34899.7
3.03-3.196.80.10823560.9950.0440.1170.38499.5
3.19-3.396.70.08923640.9960.0370.0960.42799.3
3.39-3.656.40.07323450.9970.0310.0790.47199.2
3.65-4.026.30.06123770.9970.0260.0670.57598.8
4.02-4.595.40.04822400.9980.0220.0530.57794.6
4.59-5.765.90.04521670.9980.020.0490.54689.9
5.76-206.80.03824030.9990.0160.0410.77698.1

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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: 2.14→19.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.113 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2000 4.3 %RANDOM
Rwork0.1511 ---
obs0.1531 44034 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.71 Å2 / Biso mean: 27.028 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.09 Å2
2--0.52 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 2.14→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 95 578 6910
Biso mean--25.9 33.16 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136550
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175891
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6688870
X-RAY DIFFRACTIONr_angle_other_deg1.5491.59213687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08422.749382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.641151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4371539
X-RAY DIFFRACTIONr_chiral_restr0.0760.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021419
LS refinement shellResolution: 2.14→2.191 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.242 146 -
Rwork0.212 3209 -
obs--96.1 %

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