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- PDB-6nxi: Flavin Transferase ApbE from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6nxi
TitleFlavin Transferase ApbE from Vibrio cholerae
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / ApbE / Flavin Transferase / FAD / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein flavinylation / FAD:protein FMN transferase / transferase activity / metal ion binding / plasma membrane
Similarity search - Function
T-fold / ApbE-like domains / Flavin transferase ApbE / ApbE family / ApbE-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD:protein FMN transferase / FAD:protein FMN transferase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsOsipiuk, J. / Fang, X. / Chakravarthy, S. / Juarez, O. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Conserved residue His-257 ofVibrio choleraeflavin transferase ApbE plays a critical role in substrate binding and catalysis.
Authors: Fang, X. / Osipiuk, J. / Chakravarthy, S. / Yuan, M. / Menzer, W.M. / Nissen, D. / Liang, P. / Raba, D.A. / Tuz, K. / Howard, A.J. / Joachimiak, A. / Minh, D.D.L. / Juarez, O.
History
DepositionFeb 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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_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
Revision 1.4Mar 6, 2024Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0765
Polymers36,1801
Non-polymers8964
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.121, 70.957, 106.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FAD:protein FMN transferase / Flavin transferase


Mass: 36179.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: apbE, C9J66_08705, EN12_11145, ERS013140_01021, ERS013173_02114, ERS013193_02472, ERS013199_02400, ERS013202_01888
Plasmid: pBAD/HisB / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A0F4FI39, UniProt: A5F5Y3*PLUS, FAD:protein FMN transferase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.1 M sodium acetate, 25% PEG 4000, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.61→42.7 Å / Num. obs: 38465 / % possible obs: 98.9 % / Redundancy: 7.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.037 / Rrim(I) all: 0.104 / Χ2: 1.264 / Net I/av σ(I): 22.9 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.61-1.656.10.6931.7416670.8040.2990.7580.52188.1
1.65-1.6870.65118320.8090.2620.7040.58896.6
1.68-1.717.80.56119340.8710.2150.6030.60399.9
1.71-1.757.70.50419060.8920.1930.5410.672100
1.75-1.787.70.44419290.9170.170.4770.774100
1.78-1.827.70.36818880.9370.140.3950.85399.9
1.82-1.877.70.32219360.9520.1230.3460.95899.7
1.87-1.927.10.26518590.9610.1050.2861.10897.9
1.92-1.987.90.24219430.9690.090.2591.4399.7
1.98-2.048.10.21819030.9750.080.2331.51899.9
2.04-2.1180.20119200.9740.0730.2141.69299.9
2.11-2.27.80.17919430.980.0660.1911.67499.8
2.2-2.37.30.15619150.9780.060.1681.71899.3
2.3-2.427.90.14819220.9860.0540.1581.64298.8
2.42-2.578.20.13819370.9850.050.1471.64799.9
2.57-2.778.10.12119520.9880.0440.1291.574100
2.77-3.057.50.10319650.9910.0390.1111.59299.5
3.05-3.498.30.0919740.9940.0320.0961.48699.9
3.49-4.47.70.07220120.9930.0280.0781.33299.5
4.4-42.77.50.07321280.9950.0280.0781.3999.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pnd

3pnd


Resolution: 1.61→42.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.125 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.097
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1940 5.1 %RANDOM
Rwork0.1725 ---
obs0.1745 36465 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.11 Å2 / Biso mean: 28.619 Å2 / Biso min: 17.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0 Å20 Å2
2--1.36 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.61→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 59 249 2691
Biso mean--25.9 38.45 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132557
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172359
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6523498
X-RAY DIFFRACTIONr_angle_other_deg1.4941.5765506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75823.106132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3251517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
LS refinement shellResolution: 1.614→1.656 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 122 -
Rwork0.255 2221 -
all-2343 -
obs--82.3 %
Refinement TLS params.Method: refined / Origin x: 7.3035 Å / Origin y: 32.1183 Å / Origin z: 37.8811 Å
111213212223313233
T0.0752 Å2-0.0123 Å2-0.0023 Å2-0.0293 Å20.0017 Å2--0.0035 Å2
L0.3056 °2-0.0277 °20.0385 °2-1.1968 °2-0.5103 °2--0.7459 °2
S-0.0576 Å °0.026 Å °-0.0085 Å °0.0405 Å °0.0142 Å °-0.0516 Å °-0.0582 Å °0.0559 Å °0.0434 Å °

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