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- PDB-4ovp: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4ovp
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1, TARGET EFI-510292, WITH BOUND ALPHA-D-MANURONATE
ComponentsC4-dicarboxylate transport system substrate-binding protein
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance transport / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / 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
alpha-D-mannopyranuronic acid / Solute-binding protein NAS141_03721
Similarity search - Component
Biological speciesSulfitobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionDec 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords / struct_site
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site.details
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C4-dicarboxylate transport system substrate-binding protein
B: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6194
Polymers73,2312
Non-polymers3882
Water10,827601
1
A: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8102
Polymers36,6151
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: C4-dicarboxylate transport system substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8102
Polymers36,6151
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.481, 82.345, 106.829
Angle α, β, γ (deg.)90.000, 140.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein C4-dicarboxylate transport system substrate-binding protein


Mass: 36615.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter sp. (bacteria) / Strain: NAS-14.1 / Gene: NAS141_03721 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3T0D1
#2: Sugar ChemComp-MAV / alpha-D-mannopyranuronic acid / alpha-D-mannuronic acid / D-mannuronic acid / mannuronic acid / Mannuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DManpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranuronic acidCOMMON NAMEGMML 1.0
a-D-ManpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (32.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Manuronate); Reservoir (0.1 M Tris Hydrochloride pH 8.5, 1.2 M tri-Sodium Citrate Dihydrate); Cryoprotection (Slow mount, resulting ...Details: Protein (32.6 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Manuronate); Reservoir (0.1 M Tris Hydrochloride pH 8.5, 1.2 M tri-Sodium Citrate Dihydrate); Cryoprotection (Slow mount, resulting in concentration of mother liquor prior to freezing)

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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: Nov 26, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→68.563 Å / Num. all: 77299 / Num. obs: 77299 / % possible obs: 99.3 % / Redundancy: 7.5 % / Biso Wilson estimate: 22.46 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Rsym value: 0.064 / Net I/av σ(I): 10.026 / Net I/σ(I): 17.4 / Num. measured all: 581416
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.7-1.797.51.070.9140.984424112190.3871.070.9142.198.9
1.79-1.97.60.6090.5161.580567106300.220.6090.5163.699.2
1.9-2.037.60.3440.2882.77568199590.1240.3440.2886.399.3
2.03-2.197.60.2080.1674.77113793570.0750.2080.16710.499.6
2.19-2.47.60.140.1057.56542486000.050.140.10515.799.7
2.4-2.697.60.1060.07410.45943378220.0380.1060.07421.599.9
2.69-3.17.50.0820.0514.85197269020.030.0820.0530.599.9
3.1-3.87.40.0610.03518.64330458870.0220.0610.03543.5100
3.8-5.387.30.0510.02724.33320645530.0190.0510.02752.199.9
5.38-68.5636.90.0710.02824.31626823700.0260.0710.0284993.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.872 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.888 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 3889 5.03 %
Rwork0.1491 73383 -
obs0.1507 77272 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.27 Å2 / Biso mean: 33.6532 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 26 601 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014850
X-RAY DIFFRACTIONf_angle_d1.2526575
X-RAY DIFFRACTIONf_chiral_restr0.078755
X-RAY DIFFRACTIONf_plane_restr0.007862
X-RAY DIFFRACTIONf_dihedral_angle_d12.8341826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72070.2831410.23592618275999
1.7207-1.74250.26921460.22142575272199
1.7425-1.76540.2651370.21982625276299
1.7654-1.78960.22371190.21652601272099
1.7896-1.81520.24471130.19252611272499
1.8152-1.84230.2231440.19572607275199
1.8423-1.87110.21991310.18142617274899
1.8711-1.90180.23491350.1762620275599
1.9018-1.93450.22251450.17752574271999
1.9345-1.96970.21721100.17132619272999
1.9697-2.00760.2091310.16962692282399
2.0076-2.04860.20441370.16222627276499
2.0486-2.09310.19561390.15732559269899
2.0931-2.14180.18621530.14642605275899
2.1418-2.19530.18841450.13912617276299
2.1953-2.25470.16781430.13842603274699
2.2547-2.3210.17561410.135126352776100
2.321-2.39590.18251480.138326322780100
2.3959-2.48150.19071390.14126422781100
2.4815-2.58080.21211500.149826182768100
2.5808-2.69830.19371340.156626402774100
2.6983-2.84040.20311510.156926492800100
2.8404-3.01830.17791410.161426372778100
3.0183-3.25120.20361470.154726252772100
3.2512-3.5780.16421250.141426922817100
3.578-4.0950.13791590.121826322791100
4.095-5.15640.13111390.108226762815100
5.1564-33.87860.16671460.16342535268194
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)
11.8571-0.1716-0.53110.4060.35340.56580.10460.35680.1289-0.2966-0.03-0.03640.0713-0.0422-0.02370.3040.08810.00670.25190.0210.221836.581231.498942.2888
22.46960.8174-0.78432.5206-0.49621.9375-0.09240.6040.1093-0.75910.0562-0.0223-0.0198-0.02950.03490.33670.03880.01680.32950.03550.204631.214238.532140.8119
32.1968-0.4536-0.07810.8835-0.26752.0981-0.0598-0.13310.089-0.0019-0.0215-0.0069-0.25940.01460.07920.18180.0233-0.02220.15820.03480.203928.185337.392560.8058
41.5061-0.34710.24731.3826-0.29511.05470.0043-0.2203-0.2838-0.01390.01410.25930.0306-0.1908-0.00410.13910.0173-0.01910.20080.04410.23920.358829.146264.1264
53.02680.6023-0.96880.9-0.20451.0220.17820.28480.0783-0.1616-0.0680.1935-0.2122-0.1739-0.09110.23990.0575-0.04360.20850.04940.228220.32541.095649.4197
61.6092-0.1150.85061.3201-0.29271.6836-0.3187-0.53460.44540.32360.06340.4969-0.5997-0.36480.16920.37650.0807-0.03580.3467-0.06910.396817.759241.029873.6786
70.8503-0.5875-0.69991.5121-0.10921.53570.02170.2003-0.2132-0.175-0.08130.43850.1111-0.39770.01580.21110.0086-0.0440.29-0.04870.2807-22.565753.210244.5304
82.0855-0.5105-0.98361.16610.49911.9677-0.0929-0.2193-0.06820.16640.1708-0.00720.16010.2093-0.08250.20390.0382-0.01250.2226-0.01780.194-2.848355.309653.3006
93.0031-0.9614-1.18610.78280.21141.6814-0.3272-0.3937-0.3610.26470.18260.10840.36370.20530.1290.26860.0668-0.00130.25840.01770.2416-7.137547.264555.3179
101.34440.2841-0.08311.26860.15331.21780.05030.11340.1171-0.20970.0279-0.1102-0.21080.1383-0.06770.27230.02920.0260.2034-0.00710.1773-1.144562.981143.2511
111.6433-0.0003-0.31471.2016-0.07041.20050.059-0.15470.3694-0.0566-0.1277-0.1061-0.48150.08380.02910.2714-0.01150.02180.2341-0.04730.21621.257568.092849.6261
120.9070.07890.35041.62190.28920.85150.0410.09360.0995-0.3243-0.02290.035-0.1673-0.0228-0.01970.27290.0689-0.01060.1937-0.01580.1478-9.414861.171840.639
133.38180.6639-1.92771.4998-0.4452.7732-0.0830.1261-0.4721-0.2817-0.0656-0.02090.3474-0.03870.14620.29820.0336-0.02580.1756-0.04950.1981-11.511746.313339.0381
140.33970.02680.22650.85920.03112.50090.11820.12360.0506-0.26690.0402-0.3835-0.0630.7431-0.13740.28740.04140.05140.395-0.0580.33248.361560.184846.27
152.7225-0.768-1.96613.38252.51724.20680.152-0.1804-0.39360.2730.1421-0.25140.84990.7783-0.24410.30870.1432-0.06490.3022-0.04650.24852.941949.116360.0496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 67 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 163 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 253 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 289 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 290 through 328 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 99 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 116 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 140 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 141 through 177 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 178 through 195 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 196 through 253 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 254 through 289 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 290 through 317 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 318 through 330 )B0

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