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

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Entry
Database: PDB / ID: 4pbq
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM HAEMOPHILUS INFLUENZAE RdAW (HICG_00826, TARGET EFI-510123) WITH BOUND L-GULONATE
ComponentsPutative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homologyBacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / L-gulonate / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Derived calculations / Non-polymer description
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Aug 26, 2015Group: Data collection
Revision 1.5Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
B: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
C: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,31614
Polymers114,8303
Non-polymers1,48611
Water24,6991371
1
A: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7644
Polymers38,2771
Non-polymers4873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5693
Polymers38,2771
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9837
Polymers38,2771
Non-polymers7076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.449, 76.537, 112.977
Angle α, β, γ (deg.)90.000, 114.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-541-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Putative TRAP PERIPLASMIC SOLUTE BINDING PROTEIN


Mass: 38276.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: RdAW / Gene: HICG_00826 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9MHP2

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Non-polymers , 5 types, 1382 molecules

#2: Chemical ChemComp-2UF / L-gulonate


Mass: 196.155 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (23.86 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-Gulonate); Reservoir (0.2 M Ammonium Sulfate, 0.1 M MES pH 6.5, 30 %(w/v) PEG 5000 MME); Cryoprotection (80% Reservoir + 20% diethylene 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: Mar 21, 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: 1.65→103.2 Å / Num. obs: 121100 / % possible obs: 96.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 14.08 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.055 / Net I/σ(I): 10.6 / Num. measured all: 564467 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.65-1.684.40.7192.12601258730.38295.3
9.04-103.240.06121.429547390.03390

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.65→37.111 Å / FOM work R set: 0.8932 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 11938 5.03 %Random Selection
Rwork0.1474 225248 --
obs0.1493 237186 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.07 Å2 / Biso mean: 18.87 Å2 / Biso min: 2.8 Å2
Refinement stepCycle: final / Resolution: 1.65→37.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 92 1371 8917
Biso mean--15 31.02 -
Num. residues----912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117814
X-RAY DIFFRACTIONf_angle_d1.17910560
X-RAY DIFFRACTIONf_chiral_restr0.071131
X-RAY DIFFRACTIONf_plane_restr0.0061347
X-RAY DIFFRACTIONf_dihedral_angle_d14.4243022
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 (%)
1.65-1.66870.28413810.25857379776094
1.6687-1.68840.29143670.25617289765694
1.6884-1.7090.24673810.23897470785195
1.709-1.73060.25613900.23517299768995
1.7306-1.75340.25594060.22787379778595
1.7534-1.77740.2683730.22497411778494
1.7774-1.80280.24114020.21397333773596
1.8028-1.82970.22994080.20297481788995
1.8297-1.85830.2464030.19657323772695
1.8583-1.88880.21023720.18417458783096
1.8888-1.92130.2154100.16877563797396
1.9213-1.95630.1894440.16267361780596
1.9563-1.99390.2173390.16837590792997
1.9939-2.03460.21233710.15187533790497
2.0346-2.07880.18444040.14127630803497
2.0788-2.12720.19584200.13947437785797
2.1272-2.18040.18514000.13257538793897
2.1804-2.23930.16043990.12057493789297
2.2393-2.30520.15734160.11927570798697
2.3052-2.37960.16383710.12327630800197
2.3796-2.46460.17364190.12427560797997
2.4646-2.56330.14974060.11947639804598
2.5633-2.67990.1823690.12467611798098
2.6799-2.82110.1634110.12997596800798
2.8211-2.99780.19424010.14057623802498
2.9978-3.22920.15794080.14097670807898
3.2292-3.55390.15993810.13727653803498
3.5539-4.06760.14874160.127652806898
4.0676-5.12260.15064580.11397643810199
5.1226-37.12050.19834120.16957434784696
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)
10.993-0.0959-0.25810.86580.00831.0440.0453-0.008-0.0021-0.0693-0.0234-0.14370.04190.0814-0.01670.06220.01210.00860.0266-0.00040.068722.66680.413822.4766
21.09590.0348-0.02130.93720.04620.82640.01790.1007-0.1115-0.0368-0.02150.07040.1393-0.17760.0190.082-0.0023-0.01740.02910.00830.06027.9353-4.487524.7661
30.75640.0220.05621.1719-0.02221.1751-0.0189-0.0995-0.05540.10420.03310.0556-0.0486-0.0523-0.00970.07790.00090.00260.05850.01810.06855.16282.325435.5809
40.8503-0.0743-0.69150.6052-0.02711.8531-0.0272-0.0296-0.1408-0.00150.0117-0.10490.1330.1123-0.02920.09510.0212-0.00440.0463-0.00270.085823.9797-7.494523.1038
51.1647-0.04580.44710.69280.73361.46480.0346-0.1218-0.27590.0147-0.10920.122-0.0031-0.34410.04490.1261-0.0447-0.02090.11970.04680.1914-3.7356-7.888129.6984
61.1464-1.28360.44773.6199-1.03240.82350.09840.0628-0.152-0.94250.09730.35750.3681-0.31270.00160.296-0.0541-0.07410.1956-0.03870.21952.0925-11.047910.8083
71.09370.3669-0.34391.0063-0.32281.44240.00810.16460.1367-0.07060.10430.1045-0.1666-0.2263-0.07610.09030.00640.01220.09780.02670.110722.541437.903313.2696
81.09860.1836-0.21610.7187-0.37041.2729-0.0306-0.0187-0.0201-0.0349-0.0164-0.12740.0550.1178-0.00010.0763-0.01110.01860.0777-0.0120.108134.509524.636520.5067
91.79350.41550.63570.7288-0.34561.405-0.04220.10440.06-0.0938-0.0557-0.20120.0390.47970.03990.1055-0.01340.03630.13540.01310.148941.507129.944516.9822
100.34510.0823-0.07450.4533-0.12940.69890.0323-0.06750.06650.072-0.0457-0.0843-0.09940.07940.01650.0772-0.02670.00340.0787-0.0140.087931.705830.246125.0065
111.34780.26130.2140.96170.04621.52810.0048-0.287-0.1850.20270.0463-0.06050.0456-0.0255-0.05510.09140.0038-0.02190.1120.01380.088827.507816.744436.6667
121.30540.3192-0.09960.8309-0.40410.59840.0851-0.08730.10740.1423-0.01110.034-0.1802-0.0048-0.05180.106-0.00860.00360.085-0.02250.085321.913727.172835.7128
130.73590.1149-0.17250.7446-0.51971.82860.0336-0.01020.14590.05370.014-0.0079-0.31180.0885-0.01870.1136-0.03230.03380.056-0.01180.12231.283739.244717.6256
141.408-0.1335-0.12270.9515-0.71331.337-0.0344-0.2627-0.03710.1804-0.0151-0.1649-0.020.23540.03290.149-0.0265-0.06090.181-0.01450.160937.551621.100638.5223
151.73912.22090.83533.84231.2611.1716-0.0260.1896-0.28940.10.1892-0.53850.18360.3426-0.06650.11060-0.00130.27340.00250.251348.815321.560222.1588
161.2730.07210.37620.986-0.01342.10180.0241-0.0214-0.062-0.0772-0.07220.19060.3371-0.07250.0490.10150.0137-0.02710.1066-0.00250.1019-11.722715.546618.4725
170.6098-0.3332-0.1410.5545-0.30481.61970.0266-0.027-0.084-0.1834-0.0774-0.0260.24780.07120.00320.14450.0458-0.01380.09420.00760.0731-2.50114.126619.6046
180.84260.07240.10150.5231-0.31661.0075-0.02320.00730.1457-0.1466-0.0614-0.0749-0.1110.03530.05080.06280.0228-0.01140.08960.01060.1121-0.054632.43822.6489
190.7493-0.21550.36390.7932-0.14650.6786-0.00390.14540.2183-0.1148-0.08110.0345-0.1845-0.04320.06560.08210.0205-0.01960.12650.00930.1376-5.598933.269418.7179
200.8379-0.25640.30911.4360.08360.9542-0.1029-0.16390.26140.1883-0.0849-0.027-0.2666-0.0276-0.03310.15250.0199-0.04380.09-0.06930.13761.244236.219841.3486
210.6731-0.01010.34220.87910.03231.2883-0.0037-0.13870.03750.1237-0.03040.15360.0194-0.30120.01060.07770.01350.01610.1519-0.05260.1028-6.776927.496240.6493
221.07150.35460.21410.93040.01091.36070.0125-0.06590.1482-0.1503-0.05820.1905-0.0388-0.11690.01050.04790.0369-0.03360.1137-0.00990.1054-11.477723.846617.2026
230.85350.11950.38281.0524-0.19321.8366-0.1295-0.01180.2410.1746-0.05980.0292-0.5195-0.20310.07730.21330.0548-0.06220.0904-0.0570.2681-4.693444.26436.1571
243.20580.41970.34020.79870.01370.6869-0.02850.12120.7174-0.0887-0.0684-0.2202-0.31330.07520.03790.2685-0.022-0.05760.14470.04720.3129-0.049846.231317.1241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 112 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 172 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 233 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 283 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 284 through 313 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 328 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 82 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 112 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 135 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 136 through 152 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 153 through 190 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 191 through 233 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 283 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 284 through 313 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 314 through 328 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 25 through 55 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 82 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 83 through 112 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 113 through 152 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 153 through 190 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 191 through 233 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 234 through 283 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 284 through 313 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 314 through 328 )C0

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