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- PDB-4xgv: Crystal structure of Escherichia coli Flavin trafficking protein,... -

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Basic information

Entry
Database: PDB / ID: 4xgv
TitleCrystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / FLAVIN TRANSFERASE / BIMETAL CENTER / LIPOPROTEIN
Function / homology
Function and homology information


FAD:protein FMN transferase / oxidoreductase complex / 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
ACETATE ION / FAD:protein FMN transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.883 Å
AuthorsTomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: Microbiologyopen / Year: 2016
Title: Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FAD:protein FMN transferase
B: FAD:protein FMN transferase
C: FAD:protein FMN transferase
D: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,67424
Polymers150,6024
Non-polymers1,07220
Water13,980776
1
A: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0218
Polymers37,6501
Non-polymers3707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0017
Polymers37,6501
Non-polymers3506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7764
Polymers37,6501
Non-polymers1253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8775
Polymers37,6501
Non-polymers2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.197, 70.645, 85.961
Angle α, β, γ (deg.)75.700, 72.450, 69.280
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer, as verified in vitro in solution. There are 2 biological units in the asymmetric unit.

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 37650.438 Da / Num. of mol.: 4 / Fragment: Soluble fragment, UNP residues 21-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: apbE, yojK, yojL, b2214, JW5368 / Plasmid: pET-21 NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AB85, FAD:protein FMN transferase

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Non-polymers , 5 types, 796 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M ammonium nitrate, 20% (w/v) PEG 3350, 35% (v/v) ethylene glycol;

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 91038 / Num. obs: 91038 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 21.44 Å2 / Rmerge(I) obs: 0.064 / Χ2: 1.069 / Net I/av σ(I): 13.689 / Net I/σ(I): 7.6 / Num. measured all: 190214
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.88-1.912.10.5811.844881.81894.5
1.91-1.952.10.46844731.61295.5
1.95-1.982.10.28345220.77496.7
1.98-2.032.10.25845261.04596.4
2.03-2.072.10.30244541.71494.4
2.07-2.122.10.22444881.02197
2.12-2.172.10.14246140.67897.3
2.17-2.232.10.15545691.04897
2.23-2.292.10.19643731.77193.8
2.29-2.372.10.09546070.6297.5
2.37-2.452.10.08645940.64597.5
2.45-2.552.10.08245740.71197.3
2.55-2.672.10.08345660.88597.2
2.67-2.812.10.0746110.84997.5
2.81-2.982.10.05345380.81998
2.98-3.212.10.04746290.89997.9
3.21-3.5420.04345981.14697.7
3.54-4.052.10.03745871.26697.8
4.05-5.12.10.0346530.99398.7
5.1-502.10.03345741.16597.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2O18

2o18


Resolution: 1.883→31.513 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 4544 5 %random selection
Rwork0.1626 86302 --
obs0.1645 90846 96.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.1 Å2 / Biso mean: 34.2088 Å2 / Biso min: 10.78 Å2
Refinement stepCycle: final / Resolution: 1.883→31.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9514 0 143 776 10433
Biso mean--41.75 32.93 -
Num. residues----1232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079808
X-RAY DIFFRACTIONf_angle_d0.95613219
X-RAY DIFFRACTIONf_chiral_restr0.0371502
X-RAY DIFFRACTIONf_plane_restr0.0051700
X-RAY DIFFRACTIONf_dihedral_angle_d12.6923623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8831-1.90450.39651480.29482561270985
1.9045-1.92690.3091340.25672784291893
1.9269-1.95040.28471600.2432824298495
1.9504-1.97510.24961420.19542890303296
1.9751-2.00110.22551470.18372883303097
2.0011-2.02850.22291570.18482875303296
2.0285-2.05750.24361470.18872875302297
2.0575-2.08820.22611530.19872789294292
2.0882-2.12080.19481220.16352833295597
2.1208-2.15560.19541430.15442960310397
2.1556-2.19270.19541400.15432888302897
2.1927-2.23260.2161410.17032917305897
2.2326-2.27550.23781500.18712721287191
2.2755-2.32190.21471730.15982861303497
2.3219-2.37240.22041540.14972929308397
2.3724-2.42760.17391340.14812968310298
2.4276-2.48830.19841590.14352836299598
2.4883-2.55550.21621600.14742933309397
2.5555-2.63070.17481390.15162901304098
2.6307-2.71550.20721580.16192878303697
2.7155-2.81250.21611590.15672955311498
2.8125-2.92510.21281690.16032892306198
2.9251-3.05810.17561550.16042896305198
3.0581-3.21920.1911430.16092946308998
3.2192-3.42060.18711540.1612908306298
3.4206-3.68440.18751520.15812898305097
3.6844-4.05450.19241900.14942909309998
4.0545-4.63960.14871500.13732927307799
4.6396-5.83930.18091550.15982965312099
5.8393-31.51770.20921560.16082900305697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2309-0.5023-0.24811.63380.10241.0347-0.058-0.2538-0.0140.3609-0.05630.19050.0353-0.19690.03930.2156-0.01680.07620.2411-0.02520.165943.64321.54353.1045
20.64970.7158-0.1912.25530.29220.83090.0255-0.2152-0.01810.27110.0331-0.2193-0.02180.13730.01180.15520.0128-0.03780.2633-00.214263.86217.3655-0.3079
31.07580.0873-0.09391.02610.11841.3103-0.0039-0.05290.1654-0.0715-0.05640.1287-0.2121-0.02760.07220.17690.0128-0.01290.1536-0.02710.192147.659716.277-11.4476
41.51530.79410.02493.7416-0.50361.54670.1031-0.209-0.08580.59250.01050.1620.0559-0.14530.01060.3632-0.0450.04450.19140.00610.203544.905428.4855-36.4502
52.52332.3792-1.45713.8402-1.55921.97390.0974-0.2954-0.11630.3174-0.204-0.16810.04180.14020.01620.31080.0009-0.05670.19270.00040.152655.6427.099-37.5392
61.72960.1267-1.43951.38790.68142.59110.0706-0.35810.13560.38590.0344-0.1323-0.19830.6022-0.07330.2526-0.0514-0.07620.2743-0.01210.225170.822342.2502-47.0418
71.0660.0411-0.13181.7480.40990.8105-0.0321-0.04570.1470.08240.0057-0.007-0.23650.04110.03840.1888-0.0106-0.00870.1548-0.00140.151358.506146.6552-54.9085
82.20980.0397-1.83110.8925-0.11512.28510.1269-0.47130.86010.36710.1942-0.1916-0.02770.0926-0.07650.5482-0.11750.0550.3583-0.10010.457558.652163.5265-44.8443
90.4782-0.1347-0.06240.81460.35181.0741-0.00290.03650.09290.18980.0733-0.2029-0.11220.2299-0.040.1769-0.0445-0.03270.18320.00650.193967.107242.9473-55.8912
101.3423-0.34850.51571.4191-0.10011.9505-0.0186-0.07290.00860.3342-0.00440.2850.0478-0.2444-0.02140.2287-0.02170.05870.1764-0.01590.201242.371330.4715-46.8211
110.59980.0661-0.18154.45531.83941.66130.0452-0.14050.31420.46220.0268-0.0378-0.2104-0.0018-0.01470.36580.00540.02910.1762-0.05120.378641.663654.7678-44.5045
120.7941-0.0512-0.03181.51450.42330.77880.07240.02130.20290.0252-0.05420.1661-0.28490.0034-0.03520.2748-0.00180.00750.15910.0060.239247.936151.5111-52.2476
131.66310.16560.21962.50090.27941.50470.03980.12830.19050.0601-0.06980.501-0.2292-0.27520.02190.22730.0824-0.00490.2380.02130.318636.360548.8358-56.9638
141.583-1.82090.0196.4249-0.58071.65480.08210.1128-0.0727-0.7404-0.0220.19980.3371-0.10170.0240.3860.0463-0.0230.24290.0080.197744.0602-0.0703-36.7064
151.7914-1.72411.52881.7465-1.22681.88560.18090.19020.0292-0.8317-0.2272-0.13640.57150.3163-0.01710.36990.13350.15280.26340.04120.183761.8757-6.9969-29.6124
161.0076-0.19530.3881.78770.74340.4420.08980.1683-0.1863-0.3088-0.0578-0.06030.450.15280.03480.460.0950.01540.21350.00020.207656.3181-25.6588-19.8847
170.2843-0.22040.24461.0597-0.16480.85890.04430.03840.0072-0.1758-0.1119-0.13290.18870.20850.04580.21020.05630.04040.18950.02430.153357.2153-7.6942-20.5377
181.0262-0.1363-0.52093.23030.16781.55010.02780.05690.0321-0.4643-0.01520.35660.2385-0.294-0.00570.2916-0.0033-0.08270.2188-0.02080.242834.7103-5.5023-26.035
191.0479-0.1659-0.07040.9020.12610.61130.05150.0602-0.2251-0.1007-0.04220.11450.4019-0.0514-0.02160.3985-0.0011-0.01340.161-0.01610.218643.1576-24.7329-22.8149
201.17040.38790.13652.08610.61021.07570.0748-0.1043-0.0263-0.0789-0.09710.42040.3779-0.1929-0.01310.2973-0.0908-0.01020.2091-0.00210.235833.4204-19.0573-16.2228
210.55870.0159-0.03490.7347-0.29190.9089-0.0040.1158-0.0155-0.05460.03980.03950.0709-0.1531-0.01150.0776-0.0177-0.01640.21520.01450.147249.08928.1995-74.1899
221.1246-0.6091-0.83052.1871.47071.91790.08670.2043-0.1748-0.3885-0.0205-0.05680.041-0.0737-0.07720.26410.03570.00990.2307-0.03440.199268.39612.4067-76.7483
231.13540.2945-0.28760.77810.06730.97890.00550.0648-0.00060.0368-0.01750.10830.0148-0.08750.0120.0855-0.0129-0.00620.16180.00610.149750.792627.5498-66.9815
241.979-0.2732-0.52131.2620.34991.3839-0.02250.0974-0.30750.1416-0.02420.0710.2608-0.01980.0390.2061-0.0132-0.00580.1419-0.00330.172653.59798.9426-60.9212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 81 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 167 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 328 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 13 through 35 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 57 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 81 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 112 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 136 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 137 through 167 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 168 through 230 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 231 through 250 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 251 through 289 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 290 through 329 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 13 through 35 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 36 through 81 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 136 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 137 through 192 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 193 through 236 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 237 through 289 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 290 through 329 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 13 through 97 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 98 through 136 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 137 through 209 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 210 through 329 )D0

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