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

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Basic information

Entry
Database: PDB / ID: 4xgw
TitleCrystal structure of Escherichia coli Flavin trafficking protein, an FMN transferase, E169K mutant
ComponentsFAD:protein FMN transferase
KeywordsTRANSFERASE / FLAVIN TRANSFERASE / BIMETAL CENTER / LIPOPROTEIN
Function / homology
Function and homology information


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
FAD:protein FMN transferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.747 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 1.1Dec 23, 2015Group: Derived calculations
Revision 1.2Mar 16, 2016Group: Database references
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 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation / _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)151,08015
Polymers150,6024
Non-polymers47811
Water12,232679
1
A: FAD:protein FMN transferase
C: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5518
Polymers75,3012
Non-polymers2506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-43 kcal/mol
Surface area27380 Å2
MethodPISA
2
B: FAD:protein FMN transferase
D: FAD:protein FMN transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5287
Polymers75,3012
Non-polymers2275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-32 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.216, 70.650, 86.276
Angle α, β, γ (deg.)75.720, 71.910, 69.720
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 37650.504 Da / Num. of mol.: 4 / Fragment: Soluble fragment, UNP residues 21-351 / Mutation: E169K
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
#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.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaCl, 25% (w/v) PEG 3350, 0.1 M HEPES, 20% (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: Nov 2, 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: 1.747→50 Å / Num. all: 116958 / Num. obs: 116958 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Χ2: 1.493 / Net I/av σ(I): 20.748 / Net I/σ(I): 10.3 / Num. measured all: 429538
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.783.60.8551.857481.496
1.78-1.813.60.81357831.53996.1
1.81-1.853.70.69658331.53296.2
1.85-1.893.70.61157221.57196.1
1.89-1.933.70.49158181.66296.4
1.93-1.973.70.458311.6396.6
1.97-2.023.70.31358291.2196.7
2.02-2.073.70.27357771.28296.8
2.07-2.143.70.22758191.27296.9
2.14-2.23.70.19458931.19397.4
2.2-2.283.70.18458341.51197.1
2.28-2.383.70.13858731.28897.4
2.38-2.483.70.12458681.41997.8
2.48-2.613.70.10558891.35197.8
2.61-2.783.70.09458641.51198.1
2.78-2.993.70.07459061.60698.3
2.99-3.293.60.05759121.57898.6
3.29-3.773.50.04559671.84698.7
3.77-4.753.60.03559451.78298.8
4.75-503.70.03358471.70997.4

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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: 4XGV

4xgv


Resolution: 1.747→33.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 5873 5.04 %random selection
Rwork0.1718 110687 --
obs0.1732 116560 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.48 Å2 / Biso mean: 34.1684 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.747→33.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9432 0 47 679 10158
Biso mean--50.34 31.13 -
Num. residues----1222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069671
X-RAY DIFFRACTIONf_angle_d0.87413101
X-RAY DIFFRACTIONf_chiral_restr0.0331487
X-RAY DIFFRACTIONf_plane_restr0.0041676
X-RAY DIFFRACTIONf_dihedral_angle_d12.6533579
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 (%)
1.7466-1.76640.29981880.2443192338084
1.7664-1.78720.27121760.25193667384395
1.7872-1.8090.2851680.25123637380595
1.809-1.83190.30161690.25793672384195
1.8319-1.8560.27321990.23853645384495
1.856-1.88140.29211620.23563643380596
1.8814-1.90830.24651810.21843689387095
1.9083-1.93680.2272150.20473593380896
1.9368-1.9670.22972090.19483710391996
1.967-1.99930.21151920.18193664385696
1.9993-2.03370.22171810.1823724390597
2.0337-2.07070.21871920.18313695388797
2.0707-2.11050.222180.1763692391097
2.1105-2.15360.19151960.1663659385597
2.1536-2.20040.18022170.16793720393797
2.2004-2.25160.21171790.17223667384697
2.2516-2.30790.18711880.16433759394797
2.3079-2.37030.22070.16373716392397
2.3703-2.440.20131930.16193719391298
2.44-2.51870.20951930.15863729392298
2.5187-2.60870.17822050.16763778398398
2.6087-2.71310.22881940.17643739393398
2.7131-2.83660.20892100.17723708391898
2.8366-2.9860.19012120.18083728394098
2.986-3.1730.20171920.18033799399199
3.173-3.41780.2062140.17423721393599
3.4178-3.76130.18842030.16143800400399
3.7613-4.30460.16722100.1483741395199
4.3046-5.41980.16061850.13373813399899
5.4198-33.92790.16482250.16173668389397
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)
12.2178-1.0720.16171.1345-0.27490.8464-0.0813-0.2539-0.09010.15470.03170.1033-0.0065-0.05540.04730.1895-0.01020.02710.236-0.00470.16343.70431.66073.2641
20.40990.7534-0.13672.09260.26120.83530.064-0.14080.01080.156-0.0766-0.13290.01970.09450.02220.13320.0048-0.02650.22980.01940.201964.18036.8971-0.6433
31.41560.35770.10770.735-0.01430.8274-0.0039-0.07940.2098-0.0088-0.05570.0979-0.1197-0.01350.06920.15950.0056-0.00550.1643-0.02630.169447.980116.0657-11.184
42.22611.5270.36565.0685-0.03292.10290.0208-0.1144-0.12090.35770.08690.1323-0.1214-0.1962-0.04370.3063-0.01610.03290.21280.01040.176344.800428.8447-36.3422
51.3170.9361-0.86431.0821-0.5991.71380.1471-0.21420.01640.2528-0.128-0.0869-0.12750.30850.01740.2731-0.0245-0.04370.2389-0.00550.184863.293935.2921-42.5976
61.09270.0452-0.20170.91770.25160.84710.0713-0.08620.28570.1008-0.0061-0.1084-0.23910.125-0.07080.2363-0.0432-0.00760.1694-0.03090.1959.74546.8694-51.5949
72.0919-0.41840.36121.92110.15941.95760.0366-0.1588-0.02670.3193-0.02360.2545-0.0764-0.319-0.04180.20120.00860.05640.171-0.00840.185737.83131.2011-46.5107
80.99130.61110.09242.00790.46440.96410.08570.00150.27680.2428-0.06290.2841-0.2873-0.121-0.00820.30270.03350.02730.1570.00160.266341.326151.2297-52.3597
92.357-2.12210.14876.503-0.63442.06210.02210.2451-0.1048-0.3572-0.06210.32970.27160.0050.04520.31310.02860.0190.23540.01620.17344.0682-0.1288-36.6717
102.5319-1.80331.74351.7045-1.25361.69560.19820.2660.0055-0.5048-0.2986-0.1920.43180.3870.05480.34090.0980.10850.28180.04430.180662.0046-7.1121-29.6353
111.2894-0.12350.10310.76920.06230.8990.01410.1158-0.2298-0.2166-0.0535-0.12320.42410.14890.01430.35890.06730.04250.1870.00770.192559.7679-21.2017-18.0688
120.7377-0.1806-0.37712.0565-0.24391.44940.00710.1206-0.0384-0.2407-0.07310.22250.1999-0.10890.03660.23390.0053-0.01850.1799-0.01790.149640.4361-2.6384-26.2372
131.323-0.79220.9080.543-0.51230.77560.33240.0214-0.2629-0.3293-0.00070.0640.7748-0.1709-0.06840.6982-0.0272-0.0310.2928-0.03260.312941.3532-30.1779-28.2015
140.6417-0.0048-0.03011.26920.19910.49960.14150.0131-0.1317-0.1238-0.1107-0.05360.42380.0042-0.02980.38480.0008-0.01950.1664-0.00960.183744.4131-21.1409-19.3753
151.14430.37770.14322.3730.70511.15660.1878-0.1538-0.05130.0437-0.18620.33870.3909-0.2038-0.02720.3597-0.12160.00160.24-0.01190.223733.564-19.1742-16.1325
160.29760.0502-0.0110.8206-0.1141.01990.00910.10020.0503-0.07430.00390.0950.0229-0.0840.00460.1253-0.0092-0.00840.18520.00720.153248.422327.9895-73.9767
171.6238-0.447-0.883.36511.23062.74530.0779-0.0429-0.0987-0.37560.0178-0.06850.02030.0996-0.10530.19980.0417-0.00610.2180.00480.198568.186712.4913-77.2792
181.1339-0.0446-0.41310.66920.08830.803-0.04480.1014-0.0345-0.00770.01740.0744-0.0021-0.0350.02140.0931-0.0077-0.00910.15290.00370.125650.221927.5992-66.9192
191.9321-0.8193-0.66031.19810.5811.199-0.00420.0919-0.23250.0229-0.04350.03960.1070.06210.04650.17990.0076-0.00140.1773-0.00940.170955.322310.6005-62.8783
202.93960.48810.18972.86870.51123.284-0.04390.0012-0.43620.21630.12640.0460.5155-0.00590.05960.2638-0.01220.00990.13860.01440.217849.29425.5868-55.6659
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 81 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 82 through 183 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 184 through 230 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 328 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 13 through 35 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 36 through 81 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 82 through 167 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 168 through 236 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 237 through 256 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 257 through 289 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 290 through 329 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 13 through 98 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 99 through 136 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 137 through 209 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 210 through 301 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 302 through 329 )D0

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