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- PDB-4x04: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4x04
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CITROBACTER KOSERI (CKO_04899, TARGET EFI-510094) WITH BOUND D-glucuronate
Componentssolute binding protein
KeywordsSOLUTE BINDING PROTEIN / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP/TeaA / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / metal ion binding / Uncharacterized protein
Function and homology information
Specimen sourceCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.5 Å resolution
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CITROBACTER KOSERI (CKO_04899, TARGET EFI-510094) WITH BOUND D-glucuronate
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2014 / Release: Dec 10, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 10, 2014Structure modelrepositoryInitial release
1.1Sep 27, 2017Structure modelDerived calculations / Refinement description / Source and taxonomy / Structure summaryentity / entity_src_gen / pdbx_struct_oper_list / software_entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: solute binding protein
B: solute binding protein
C: solute binding protein
D: solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,13216
Polyers147,0944
Non-polymers1,03812
Water18,3751020
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)175.000, 175.000, 125.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP 41 21 2
Detailsbiological unit is a monomer

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Components

#1: Protein/peptide
solute binding protein


Mass: 36773.602 Da / Num. of mol.: 4 / Fragment: solute binding protein / Source: (gene. exp.) Citrobacter koseri (bacteria) / Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_04899 / Plasmid name: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8AR30
#2: Chemical
ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 4 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Formula: Cl / Chloride
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1020 / Formula: H2O / Water

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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: 3.27 / Density percent sol: 62.38 %
Crystal growTemp: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (43.2 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 5% Glycerol, 10 mM D-glucuronate); Reservoir (0.2 M Magnesium Chloride, 20 %(w/v) PEG 3350, 0.1M Tris pH 8.5); Cryoprotection (80%(50%) PEG 3350,20% Reservoir)

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54056
DetectorType: RIGAKU RAXIS IV / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Nov 12, 2014
RadiationMonochromator: GRAPHITE / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 14.42 Å2 / D resolution high: 2.5 Å / D resolution low: 5 Å / Number obs: 94018 / Rmerge I obs: 0.102 / Chi squared: 0.97 / NetI over av sigmaI: 24.586 / NetI over sigmaI: 9.2 / Number measured all: 803840 / Redundancy: 11.9 % / Percent possible obs: 99.8
Reflection shell

Diffraction ID: 1 / Rejects: 0

Rmerge I obsHighest resolutionLowest resolutionNumber unique allChi squaredRedundancyPercent possible all
0.4012.5002.54032970.9679.60099.500
0.3622.5402.59033140.9709.70099.600
0.3452.5902.64033400.9609.70099.700
0.2992.6402.69033580.9839.80099.700
0.2702.6902.75033110.99710.00099.700
0.2432.7502.82033331.01610.10099.700
0.2362.8202.89033481.01110.40099.800
0.2092.8902.96033501.03710.70099.900
0.1852.9603.05033451.03911.000100.000
0.1583.0503.15033751.04111.400100.000
0.1413.1503.26033781.03911.800100.000
0.1203.2603.39033621.03212.300100.000
0.0973.3903.55033701.03412.800100.000
0.0893.5503.73033901.08213.200100.000
0.0753.7303.97034030.96813.800100.000
0.0583.9704.27034020.84714.300100.000
0.0504.2704.70034290.79914.500100.000
0.0524.7005.38034460.80414.500100.000
0.0635.3806.78034920.87114.400100.000
0.0526.78050.00036451.03813.10099.000

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4N8Y
Overall SU ML: 0.23 / R Free selection details: Random / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 18.34 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 83.46 Å2 / B iso mean: 18.2322 Å2 / B iso min: 0.95 Å2
Least-squares processR factor R free: 0.2048 / R factor R work: 0.1538 / R factor obs: 0.1564 / Highest resolution: 2.5 Å / Lowest resolution: 40.73 Å / Number reflection R free: 4665 / Number reflection R work: 89353 / Number reflection obs: 94018 / Percent reflection R free: 4.96 / Percent reflection obs: 95.13
Refine hist #finalHighest resolution: 2.5 Å / Lowest resolution: 40.73 Å / B iso mean ligand: 12.06 / B iso mean solvent: 23.53 / Number residues total: 1204
Number of atoms included #finalProtein: 9372 / Nucleic acid: 0 / Ligand: 60 / Solvent: 1020 / Total: 10452
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089608
X-RAY DIFFRACTIONf_angle_d1.10912984
X-RAY DIFFRACTIONf_chiral_restr0.0421448
X-RAY DIFFRACTIONf_plane_restr0.0061688
X-RAY DIFFRACTIONf_dihedral_angle_d14.3493616
Refine LS shell

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

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.20000.26890.22452.2250951995209065.0000
2.22500.26970.22402.25121102139224969.0000
2.25120.27270.21402.27871252340246575.0000
2.27870.25580.20452.30751342525265982.0000
2.30750.25880.19982.33791362700283687.0000
2.33790.24790.19542.36991402863300392.0000
2.36990.25460.18052.40371412971311296.0000
2.40370.24240.18042.43961282978310696.0000
2.43960.22650.18182.47771693048321797.0000
2.47770.22980.18842.51831553006316198.0000
2.51830.24190.17892.56181673064323199.0000
2.56180.22880.16612.60831723083325599.0000
2.60830.23540.16452.65851703077324799.0000
2.65850.21090.15622.712715930893248100.0000
2.71270.22700.15142.771717430913265100.0000
2.77170.20500.16262.836216931173286100.0000
2.83620.21700.15972.907114631203266100.0000
2.90710.24310.16242.985716831063274100.0000
2.98570.21690.16573.073517031003270100.0000
3.07350.21050.15633.172717331223295100.0000
3.17270.21590.15163.286017031113281100.0000
3.28600.17020.15013.417515531473302100.0000
3.41750.19230.14073.573017831433321100.0000
3.57300.19940.13763.761217831043282100.0000
3.76120.16810.12573.996717331633336100.0000
3.99670.15800.11354.304915231723324100.0000
4.30490.13660.10734.737614831893337100.0000
4.73760.15700.11515.421716432103374100.0000
5.42170.17310.13686.825616132533414100.0000
6.82560.17910.148040.73691853327351298.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.0091-0.0014-0.00050.0085-0.00080.00070.02870.00230.0267-0.00640.0101-0.0170-0.01890.00260.03590.02840.00810.09350.0421-0.00050.0321212.1269142.1547-10.1727
20.00050.0000-0.00050.00040.00070.0010-0.0117-0.00220.00120.01140.0039-0.0158-0.0077-0.00290.00000.06710.02260.00140.0979-0.01160.0468209.2444130.84471.6768
30.0028-0.00380.00150.0134-0.00420.00360.0087-0.01630.0105-0.0031-0.0225-0.0111-0.0104-0.0008-0.0098-0.03410.0379-0.00520.0200-0.03330.0678193.9428139.27621.1341
40.0008-0.00100.00190.00110.00240.00540.0001-0.01040.01040.0086-0.00850.00770.00340.0042-0.00640.03490.00200.00570.0463-0.05380.0630200.3308145.42046.2095
50.00100.0004-0.00210.0031-0.00180.0028-0.0111-0.0005-0.0176-0.0045-0.02260.01190.0168-0.0114-0.00080.04230.01340.00900.0840-0.05300.1088184.8414121.7296-6.7565
60.00300.0023-0.00020.00140.00230.00210.0016-0.0098-0.01630.00660.01100.00390.0041-0.00180.01550.00710.02950.02820.03620.01270.0691190.0209121.19433.2944
70.0124-0.0067-0.00900.00640.00340.00530.0178-0.0327-0.04790.00230.0105-0.00940.00470.03900.00000.05150.0054-0.00080.0829-0.00710.0933198.4175128.2441-5.4625
80.0150-0.0064-0.01380.0091-0.00180.01380.02470.0272-0.0070-0.04270.01560.0307-0.0476-0.02180.00100.0742-0.00180.01150.0772-0.01340.0899193.2401136.9003-10.3336
90.0067-0.0025-0.00390.0081-0.00610.0110-0.0003-0.01400.00800.0046-0.00450.0023-0.00530.0047-0.00400.05430.0280-0.00290.0972-0.04990.1014182.7381140.19728.9785
100.0015-0.0008-0.00040.00990.00540.00220.01510.0095-0.0221-0.01020.0045-0.01730.01110.01760.02230.0846-0.00590.00160.1116-0.1135-0.0014226.4632137.761521.3712
110.0007-0.0007-0.00080.00150.00070.00100.0096-0.0055-0.0025-0.00140.0014-0.0006-0.00670.00300.00400.0588-0.0408-0.00250.0283-0.00160.0324214.8488142.860131.8175
120.0362-0.00740.01160.0160-0.00220.0021-0.04530.02880.05050.01060.0129-0.0354-0.05280.0685-0.01100.0292-0.13130.0095-0.04460.03270.0326226.9294154.529333.0903
130.0158-0.00030.00750.03220.01100.0162-0.0069-0.00040.01330.0026-0.03070.0252-0.0543-0.0089-0.00370.1818-0.0098-0.0493-0.0119-0.08460.0058209.1216165.845726.3745
140.01700.01900.03230.06080.06440.0965-0.08250.03090.0190-0.0734-0.02340.0557-0.07180.0646-0.17350.0484-0.0541-0.0753-0.0162-0.0887-0.0863217.9408155.578622.1806
150.00740.0010-0.00420.00580.00200.0056-0.0115-0.00450.00810.0025-0.00460.0026-0.01920.0027-0.00490.1721-0.0880-0.04290.0866-0.03550.1294226.7150168.336938.3276
160.0019-0.00060.00050.00180.00070.00090.00220.0047-0.0062-0.00620.01220.01110.0141-0.0075-0.00000.0634-0.0022-0.02690.0936-0.00130.0872138.9492121.5849-9.6682
170.0038-0.00080.00020.0002-0.00040.0068-0.00770.00310.0046-0.0011-0.0091-0.00090.0027-0.0141-0.01400.0241-0.0176-0.02780.0486-0.00100.0802134.0369123.8332-6.5140
180.00120.00040.00110.00100.00080.0011-0.00720.00670.0017-0.0217-0.0211-0.0245-0.00720.0344-0.01880.00920.00490.00240.0458-0.00540.0413149.9099127.98733.9915
190.00460.00490.00340.01440.00760.00480.0193-0.0047-0.0155-0.00820.0126-0.02220.01770.00020.01770.02130.0074-0.00020.05640.01440.0571156.7406116.73492.1731
200.0067-0.00010.00710.0009-0.00270.00420.00290.00750.02220.0097-0.0099-0.04020.01760.0124-0.00000.0575-0.0079-0.00100.08320.00900.1014156.7187132.9103-1.6908
210.0018-0.0010-0.00270.0024-0.00080.0073-0.0134-0.01630.00550.0086-0.0018-0.00660.00160.0020-0.01160.00850.0312-0.02140.0675-0.02940.0691160.3357141.67152.7500
220.0118-0.0085-0.00110.01210.0056-0.00030.0213-0.01550.0466-0.00040.01610.03590.0156-0.0249-0.00000.0432-0.00300.00130.08520.00240.0865151.3058135.8838-4.7937
230.00850.00160.0107-0.00030.00080.0099-0.00470.0471-0.0110-0.0156-0.0060-0.00090.00980.03540.00000.0681-0.00410.00380.1072-0.00080.0651149.6785120.2293-10.9936
240.00880.0032-0.00140.0049-0.00060.0024-0.0091-0.00120.0083-0.00270.0072-0.00370.0003-0.0044-0.00290.01570.01540.00240.07700.01980.0677168.6139135.8125-1.4224
250.0016-0.00010.00080.00070.00100.00160.0050-0.00410.00050.0050-0.0100-0.00300.00080.00410.00000.06200.0193-0.00060.10700.00880.1582166.7465119.44159.0175
260.00490.00080.00320.00390.00080.00590.0181-0.01060.01260.01120.0238-0.0228-0.01080.03600.03220.1120-0.03890.00610.1331-0.08790.0334228.4962127.09199.0934
270.0043-0.0001-0.00180.00070.00090.00230.0271-0.00030.0088-0.0113-0.01140.00440.01000.02840.00000.06880.0207-0.01020.05920.01020.0689219.8643118.3068-2.9971
280.0146-0.00040.01310.0005-0.00060.01030.0132-0.0156-0.0321-0.00170.0190-0.01260.02270.02670.03790.01970.0866-0.03030.00010.0782-0.0218229.4103108.3986-2.0464
290.0081-0.00960.00530.0145-0.00260.0082-0.0026-0.0030-0.0148-0.00050.00440.00880.01760.0004-0.00040.10010.01830.01020.0677-0.00300.0832208.092399.46988.9005
300.00140.0028-0.00030.0053-0.00060.00200.01690.0066-0.0073-0.00210.00130.01750.0182-0.00060.00400.11030.0441-0.05970.00760.01200.0679206.8429104.1407-1.2798
310.0010-0.0023-0.00450.01200.00840.00670.0237-0.02020.02440.00890.00880.03750.01240.02660.00000.07580.0043-0.00380.07330.00400.0787214.2973112.99646.3671
32-0.00060.0028-0.00410.0023-0.00410.00820.00830.0023-0.00920.02940.0152-0.00510.01770.03760.02760.07660.0438-0.01490.04920.0568-0.0379228.8736114.501011.7642
33-0.0008-0.0005-0.00330.01820.00070.00360.0344-0.0078-0.0161-0.01930.00630.01800.0176-0.00460.01290.17780.0239-0.04510.01140.01180.0868213.597494.99363.2404
340.00050.00030.00080.00130.00010.0007-0.01430.0029-0.0033-0.0090-0.00870.0096-0.0082-0.0035-0.00000.23470.0879-0.01620.16270.00050.1907229.897096.5613-7.6817
Refine TLS group

Beg auth seq ID: 0 / End auth seq ID: 0 / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDEnd auth asym IDRefine TLS IDSelection details
1AA1chain 'A' and (resid 27 through 66 )
2AA2chain 'A' and (resid 67 through 83 )
3AA3chain 'A' and (resid 84 through 124 )
4AA4chain 'A' and (resid 125 through 148 )
5AA5chain 'A' and (resid 149 through 167 )
6AA6chain 'A' and (resid 168 through 195 )
7AA7chain 'A' and (resid 196 through 253 )
8AA8chain 'A' and (resid 254 through 305 )
9AA9chain 'A' and (resid 306 through 327 )
10BB10chain 'B' and (resid 27 through 66 )
11BB11chain 'B' and (resid 67 through 83 )
12BB12chain 'B' and (resid 84 through 148 )
13BB13chain 'B' and (resid 149 through 187 )
14BB14chain 'B' and (resid 188 through 305 )
15BB15chain 'B' and (resid 306 through 327 )
16CC16chain 'C' and (resid 27 through 56 )
17CC17chain 'C' and (resid 57 through 73 )
18CC18chain 'C' and (resid 74 through 114 )
19CC19chain 'C' and (resid 115 through 136 )
20CC20chain 'C' and (resid 137 through 167 )
21CC21chain 'C' and (resid 168 through 187 )
22CC22chain 'C' and (resid 188 through 253 )
23CC23chain 'C' and (resid 254 through 288 )
24CC24chain 'C' and (resid 289 through 313 )
25CC25chain 'C' and (resid 314 through 327 )
26DD26chain 'D' and (resid 27 through 66 )
27DD27chain 'D' and (resid 67 through 107 )
28DD28chain 'D' and (resid 108 through 148 )
29DD29chain 'D' and (resid 149 through 167 )
30DD30chain 'D' and (resid 168 through 195 )
31DD31chain 'D' and (resid 196 through 253 )
32DD32chain 'D' and (resid 254 through 288 )
33DD33chain 'D' and (resid 289 through 313 )
34DD34chain 'D' and (resid 314 through 327 )

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