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

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Entry
Database: PDB / ID: 4pet
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM COLWELLIA PSYCHRERYTHRAEA (CPS_0129, TARGET EFI-510097) WITH BOUND CALCIUM AND PYRUVATE
ComponentsExtracellular solute-binding protein, family 7
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


tripartite ATP-independent periplasmic transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function
Solute binding protein, TakP-like / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRUVIC ACID / Extracellular solute-binding protein, family 7
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / 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
DepositionApr 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular solute-binding protein, family 7
B: Extracellular solute-binding protein, family 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5607
Polymers83,2682
Non-polymers2925
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-71 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.827, 70.249, 154.927
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 Extracellular solute-binding protein, family 7


Mass: 41634.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_0129 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48AL6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 1.82 Å3/Da / Density % sol: 32.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (74.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Glycerate); Reservoir (0.1 M HEPES pH 7.0, 30 %(v/v) Jeffamine ED-2001 pH 7.0); Cryoprotection (80% Reservoir, 20% Ethylene glycol)

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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: Apr 9, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→77.46 Å / Num. obs: 48462 / % possible obs: 99.2 % / Redundancy: 13.8 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.027 / Net I/σ(I): 27.1 / Num. measured all: 667408 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.9-1.949.60.9262.32680527860.29990.4
9.11-77.4611.30.068256925030.01795.7

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.255 Å / FOM work R set: 0.8354 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 4612 5.04 %Random Selection
Rwork0.1536 86842 --
obs0.1563 91454 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.92 Å2 / Biso mean: 31.39 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: final / Resolution: 1.9→34.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 21 477 5740
Biso mean--29.38 37.01 -
Num. residues----657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145410
X-RAY DIFFRACTIONf_angle_d1.2867321
X-RAY DIFFRACTIONf_chiral_restr0.075739
X-RAY DIFFRACTIONf_plane_restr0.007934
X-RAY DIFFRACTIONf_dihedral_angle_d13.991983
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 (%)
1.9-1.92170.33411200.30082264238477
1.9217-1.94430.31671270.25622897302498
1.9443-1.9680.32541670.24032885305299
1.968-1.99290.30971360.22592977311399
1.9929-2.01920.26471560.21422810296699
2.0192-2.04680.26351990.20442874307399
2.0468-2.07610.29451380.20642972311099
2.0761-2.1070.24591420.19852868301099
2.107-2.140.23591600.19382986314699
2.14-2.1750.25891370.18782858299599
2.175-2.21250.24641800.18912906308699
2.2125-2.25280.26561630.17612911307499
2.2528-2.29610.20481610.163629183079100
2.2961-2.34290.21981750.166528863061100
2.3429-2.39390.23491810.15528973078100
2.3939-2.44950.24311830.14892888307199
2.4495-2.51080.29011330.156529553088100
2.5108-2.57870.25371530.157929363089100
2.5787-2.65450.20961450.15962944308999
2.6545-2.74010.2281290.156329203049100
2.7401-2.8380.22551760.149828933069100
2.838-2.95160.23211360.15592957309399
2.9516-3.08590.2341430.159829883131100
3.0859-3.24840.23721440.151228743018100
3.2484-3.45180.1811410.140829743115100
3.4518-3.7180.1771890.130529003089100
3.718-4.09160.14491510.116229373088100
4.0916-4.68240.10731660.107129283094100
4.6824-5.89440.19921330.130729243057100
5.8944-34.26070.19461480.16752915306399
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)
11.05450.125-0.32381.2149-0.14271.37410.0115-0.0913-0.15850.07620.0127-0.19460.1520.1087-0.03550.13620.0138-0.04860.14640.00850.201536.309510.8198109.8725
20.639-0.2318-0.06780.9383-0.38711.0006-0.04890.0363-0.007-0.01890.09920.10250.0043-0.1288-0.04070.1559-0.0298-0.02130.190.04580.170617.999812.4715106.8675
30.8103-0.0955-0.17340.9361-0.06271.3663-0.0783-0.0426-0.0892-0.01070.10280.04340.3210.0146-0.04870.255-0.0612-0.05530.22610.03470.225817.4629-0.3031101.155
41.33140.05360.31960.9445-0.13710.9302-0.04370.01960.0188-0.0670.0983-0.0206-0.00930.0103-0.05660.1463-0.0147-0.0180.14920.01860.1732.378117.1874102.6774
50.70740.179-0.17480.89550.59081.1406-0.0937-0.0391-0.0404-0.0165-0.02080.26330.1414-0.14240.14350.2334-0.0668-0.05430.32160.04920.2766.40697.356103.7929
60.91440.0095-0.11661.3857-0.7772.77360.1220.28-0.0182-0.14410.09320.3027-0.0576-0.6849-0.21570.17320.0457-0.03510.32340.03150.235911.161625.3635102.7036
71.6391-0.49170.31431.1763-0.29941.526-0.0237-0.18780.46470.0726-0.0293-0.3731-0.56170.1536-0.00610.2844-0.072-0.0010.1676-0.01820.252537.637339.6578100.7876
81.2320.10540.10621.2444-0.02730.5498-0.04280.18940.1533-0.34380.07270.0427-0.2279-0.0743-0.02550.3165-0.0164-0.00830.19870.04440.167529.314337.277285.8751
91.3436-0.4112-0.49360.5656-0.77812.14980.0079-0.02180.40560.1752-0.257-0.419-0.78480.49840.42570.6681-0.2288-0.25010.49090.24280.463418.482544.844477.5491
100.3493-0.1011-0.35350.4539-0.92542.8873-0.40420.2040.9864-0.2096-0.12960.3647-1.17250.48320.26650.5504-0.0234-0.24410.22180.11670.600212.711948.033490.5294
111.03490.36610.23790.8531-0.10891.59360.08940.07730.1086-0.0930.00230.0111-0.2369-0.1072-0.0850.21060.0089-0.00390.1360.02020.176129.943533.189695.3571
122.2023-0.0483-0.18120.8512-0.01280.9320.00450.3670.1899-0.30370.02060.2239-0.1077-0.1979-0.02090.407-0.0393-0.11530.33760.06660.34812.132134.708377.6707
131.36381.02-0.88931.7506-0.85380.9625-0.2180.344-0.0979-0.52650.25160.16440.3379-0.4779-0.06760.2968-0.0648-0.06880.32450.0370.189219.986119.415883.5702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 113 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 181 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 244 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 295 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 327 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 359 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 63 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 181 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 202 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 236 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 237 through 295 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 296 through 327 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 328 through 359 )B0

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