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- PDB-4mco: Crystal structure of a TRAP periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4mco
TitleCrystal structure of a TRAP periplasmic solute binding protein from Rhodoferax ferrireducens (Rfer_1840), target EFI-510211, with bound malonate
ComponentsTRAP dicarboxylate transporter-DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics
Function / homology
Function and homology information


organic substance transport / transmembrane transport / periplasmic space
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Solute-binding protein Rfer_1840
Similarity search - Component
Biological speciesRhodoferax ferrireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter-DctP subunit
B: TRAP dicarboxylate transporter-DctP subunit
C: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2488
Polymers113,4653
Non-polymers7835
Water25,2931404
1
A: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4004
Polymers37,8221
Non-polymers5793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9242
Polymers37,8221
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRAP dicarboxylate transporter-DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9242
Polymers37,8221
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.108, 97.107, 133.027
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 TRAP dicarboxylate transporter-DctP subunit / TRAP periplasmic solute binding protein


Mass: 37821.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodoferax ferrireducens (bacteria) / Strain: T118 / Gene: Rfer_1840 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q21XD7
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1404 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mg/mL protein in 10 mM HEPES, pH 7.5, 10 mM malonate, reservoir: MCSG1 G7 (0.1 M Tris, pH 8.5, 25% w/v PEG3350), cryoprotectant: 4:1 50% PEG8000:reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 23, 2013 / Details: mirrors
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→78.433 Å / Num. all: 128663 / Num. obs: 128663 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 13.92 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.695.80.6891.1107972185590.689100
1.69-1.796.50.491.6114379176430.49100
1.79-1.916.70.3352.3110513165710.335100
1.91-2.076.90.2063.8105947154540.206100
2.07-2.2670.1375.6100425142640.137100
2.26-2.537.30.0977.993889129220.097100
2.53-2.927.30.0710.784055114710.07100
2.92-3.587.30.04714.87092597680.047100
3.58-5.067.10.03418.85431476230.034100
5.06-133.0276.80.027222974643880.02799.8

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→32.702 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.9052 / SU ML: 0.14 / σ(F): 0 / σ(I): 0 / Phase error: 16.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 6454 5.02 %RANDOM
Rwork0.1487 ---
all0.1503 128550 --
obs0.1503 128550 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.98 Å2 / Biso mean: 20.9272 Å2 / Biso min: 4.97 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 51 1404 8763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097524
X-RAY DIFFRACTIONf_angle_d1.21810121
X-RAY DIFFRACTIONf_chiral_restr0.0681102
X-RAY DIFFRACTIONf_plane_restr0.0061289
X-RAY DIFFRACTIONf_dihedral_angle_d13.8482846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.61820.25072260.220240044230
1.6182-1.63720.24182060.211840584264
1.6372-1.65720.22752240.199439734197
1.6572-1.67820.23182170.188440374254
1.6782-1.70020.25442220.190640124234
1.7002-1.72350.24611800.182440644244
1.7235-1.74820.24712020.175540254227
1.7482-1.77420.22132130.17540474260
1.7742-1.8020.22081980.170140424240
1.802-1.83150.21182120.163340784290
1.8315-1.86310.19581890.157440364225
1.8631-1.8970.19231940.161140334227
1.897-1.93340.20912080.160540644272
1.9334-1.97290.22341980.16240554253
1.9729-2.01580.20892250.157640474272
2.0158-2.06270.19282200.153340524272
2.0627-2.11430.19892230.151340384261
2.1143-2.17140.18432240.142840134237
2.1714-2.23530.17972010.138640984299
2.2353-2.30740.15812100.133540824292
2.3074-2.38990.17771950.133540814276
2.3899-2.48550.14442310.133340594290
2.4855-2.59860.17412300.137340574287
2.5986-2.73550.17542280.138140784306
2.7355-2.90680.16212300.142840874317
2.9068-3.13110.17582280.146541094337
3.1311-3.44590.17081970.141441314328
3.4459-3.94380.13432260.13441424368
3.9438-4.9660.15162350.127241744409
4.966-32.70850.18432620.153943204582
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)
11.0566-0.17410.07770.5094-0.43071.98030.1382-0.2593-0.10270.4555-0.0051-0.16720.076-0.09310.31930.2964-0.0431-0.11040.11890.03080.123624.878343.091979.0362
20.6799-0.0819-0.01420.8437-0.11090.4246-0.0369-0.0261-0.12430.2089-0.0179-0.37010.0440.0296-0.04780.13080.0111-0.09040.05480.04430.245926.149534.261967.9218
30.65350.09180.08940.8147-0.03950.54630.01520.0228-0.1220.05110.03230.02750.0374-0.0577-0.02960.0848-0.0008-0.00450.05630.00810.098614.068736.659460.1138
40.44260.24930.0740.7214-0.07310.3839-0.0021-0.0093-0.05580.07670.0126-0.116-0.00940.0187-0.02770.09640.0101-0.01370.06550.01360.099420.536944.639961.7123
50.7653-0.43390.33961.3857-1.10251.170.015-0.1894-0.00190.4982-0.04280.0281-0.1005-0.1099-0.06620.2807-0.03080.00020.11330.0230.082215.653642.041776.5606
60.86480.26420.20191.74640.67640.8397-0.05710.10180.0991-0.11340.00380.5337-0.0233-0.18230.0040.1069-0.0058-0.030.1260.02290.18254.416845.306154.136
72.05240.187-0.55891.0376-0.42921.19480.0218-0.0337-0.2301-0.0220.02060.19320.0287-0.0296-0.07250.1282-0.02380.00910.0740.00190.23376.223326.155359.3717
81.6496-0.37490.43561.8823-0.39112.4060.0373-0.12450.24640.0719-0.0252-0.0351-0.1364-0.06570.00040.0583-0.0030.02550.1053-0.02840.0894-6.365736.795417.765
91.2362-0.1546-0.32990.34680.11490.85370.03750.00230.0394-0.0082-0.03970.0344-0.0548-0.060.01310.0619-0.00510.01160.0771-0.01230.0671-3.718631.273610.5287
101.222-0.1277-0.13690.4261-0.01490.7837-0.0573-0.2046-0.17930.08730.02020.00420.07940.06310.01530.08990.00620.01540.11090.02810.07294.887122.199717.0515
110.79760.0352-0.05510.8458-0.67962.0370.009-0.16280.14160.13980.0834-0.0143-0.29620.1255-0.0950.104-0.00260.02240.1257-0.04470.10885.665337.651915.5256
120.75250.58840.2480.580.63131.7496-0.1148-0.3398-0.24660.18890.1377-0.14210.10380.39590.0650.16690.0824-0.02010.31380.08470.164718.359117.024122.5865
131.61340.3289-0.00810.7181-0.10970.8249-0.0645-0.0233-0.17020.01560.0979-0.02210.11870.2011-0.00330.09810.00820.04450.1472-0.04990.137715.539117.42863.1733
140.7975-0.1238-0.09391.7314-0.09820.71470.0171-0.00010.20.10580.0521-0.0287-0.135-0.0601-0.05060.1041-0.00210.03530.10190.04050.118221.1014-6.18547.2266
150.91560.0007-0.61991.3667-0.78682.5898-0.01990.2473-0.017-0.13520.03720.04530.0794-0.2711-0.03460.09710.00230.00320.20150.03430.098515.1397-12.354433.1181
160.14410.0645-0.10370.2356-0.01330.36370.03840.19660.0928-0.1758-0.0505-0.04020.0414-0.0062-0.01870.150.02830.04550.18350.05090.078827.7119-14.14629.1567
170.95540.0235-0.0760.4347-0.41390.81830.09280.3526-0.0744-0.3097-0.0318-0.11480.16090.02530.20310.1730.02060.08520.17450.05870.082833.3445-19.471130.5998
180.4425-0.0402-0.13380.7857-0.23740.41020.00270.1267-0.0548-0.13880.02040.00050.1034-0.0359-0.03630.1193-00.0260.12070.02260.090726.5737-22.946837.8812
190.4893-0.2350.11492.1252-0.52850.5990.02640.01550.08790.251-0.0296-0.071-0.04190.05190.00880.1066-0.01850.03830.12150.03830.135232.1312-10.210145.2747
200.9598-0.0061-0.17690.5046-0.18171.49910.05380.1261-0.0904-0.21-0.091-0.20830.07720.2136-0.01070.23160.06230.09750.16510.02090.22242.1551-30.248433.4982
210.62270.2584-0.29190.4256-0.07550.38180.0420.13040.0958-0.0812-0.0666-0.05240.0081-0.09450.05130.22060.05990.11870.28780.11250.13241.325-14.035320.5768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 62 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 119 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 187 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 257 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 292 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 314 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 315 through 345 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 45 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 119 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 120 through 257 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 258 through 293 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 294 through 314 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 315 through 344 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 28 through 71 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 72 through 88 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 89 through 119 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 120 through 187 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 188 through 257 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 258 through 292 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 293 through 314 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 315 through 345 )C0

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