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- PDB-5i7i: Crystal structure of a marine metagenome TRAP solute binding prot... -

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Basic information

Entry
Database: PDB / ID: 5i7i
TitleCrystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-crystallized 3-hydroxybenzoate
ComponentsTRAP solute Binding Protein
KeywordsTRANSPORT PROTEIN
Function / homologyBacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / 3-HYDROXYBENZOIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesuncultured marine bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
CitationJournal: To Be Published
Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_ ...Title: Crystal structure of a marine metagenome TRAP solute binding protein specific for aromatic acid ligands (Sorcerer II Global Ocean Sampling Expedition, unidentified microbe, locus tag GOS_1523157) in complex with co-purified 4-hydroxybenzoate
Authors: Vetting, M.W. / Al Obaidi, N.F. / Hogle, S.L. / Dupont, C.L. / Almo, S.C.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAP solute Binding Protein
B: TRAP solute Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4906
Polymers74,0012
Non-polymers4884
Water20,2311123
1
A: TRAP solute Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2453
Polymers37,0011
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP solute Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2453
Polymers37,0011
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.091, 82.588, 75.961
Angle α, β, γ (deg.)90.000, 98.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRAP solute Binding Protein


Mass: 37000.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine bacterium (environmental samples)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-3HB / 3-HYDROXYBENZOIC ACID / 3-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1123 / 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: 1.93 Å3/Da / Density % sol: 36.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 75 mg/ml); Reservoir (MCSG2 A2)(0.1 M HEPES pH 7.5, 20 %(w/v) PEG 8000); Cryoprotection (20% Diethylene Glycol, 80% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→82.59 Å / Num. obs: 133576 / % possible obs: 96.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3230.7271920863070.5830.4840.8781.992.5
7.12-82.593.40.02526267650.9990.0160.0328.885.5

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Intial model obtained from a TrimethylLeadAceate Derivative dataset

Resolution: 1.3→37.575 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.49
RfactorNum. reflection% reflection
Rfree0.1726 6623 4.96 %
Rwork0.1477 --
obs0.149 133540 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.92 Å2 / Biso mean: 13.4885 Å2 / Biso min: 3.74 Å2
Refinement stepCycle: final / Resolution: 1.3→37.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4834 0 64 1125 6023
Biso mean--14.95 24.8 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085123
X-RAY DIFFRACTIONf_angle_d1.0076950
X-RAY DIFFRACTIONf_chiral_restr0.074769
X-RAY DIFFRACTIONf_plane_restr0.009896
X-RAY DIFFRACTIONf_dihedral_angle_d18.091923
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 (%)
1.3-1.31480.28162210.2624044426592
1.3148-1.33030.27112390.25724009424892
1.3303-1.34650.24922120.25134028424093
1.3465-1.36350.27852010.24164086428794
1.3635-1.38150.26842000.24154133433394
1.3815-1.40040.24742040.23284110431494
1.4004-1.42040.23872230.21394146436996
1.4204-1.44160.23512340.20364191442596
1.4416-1.46410.22432280.19794136436496
1.4641-1.48810.21942320.18734219445197
1.4881-1.51380.20932320.18054176440897
1.5138-1.54130.20682330.17384246447997
1.5413-1.5710.18392120.16334214442697
1.571-1.6030.22090.16584286449597
1.603-1.63790.18052310.15844216444798
1.6379-1.6760.17862310.14714264449598
1.676-1.71790.17192250.14224314453998
1.7179-1.76440.16761890.13644285447498
1.7644-1.81630.16162030.13884315451898
1.8163-1.87490.15422130.13934240445397
1.8749-1.94190.16722230.13784327455099
1.9419-2.01960.14252380.1354266450498
2.0196-2.11160.16862440.12534299454398
2.1116-2.22290.13452220.1234278450098
2.2229-2.36210.15032100.12154352456299
2.3621-2.54450.15852460.12024317456399
2.5445-2.80040.15062370.12374324456199
2.8004-3.20550.13052100.123543974607100
3.2055-4.03780.15092130.11864400461399
4.0378-37.59020.15162080.13534299450796
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)
11.30070.7831-0.89951.9738-0.28171.6968-0.0023-0.0426-0.02190.0286-0.0264-0.21640.10640.14550.06010.06310.0102-0.00940.06410.00210.05387.5168-0.1709-26.1666
20.1057-0.03950.47850.015-0.18352.2353-0.1217-0.30030.03610.2070.1919-0.14150.14140.2424-0.00370.12470.0415-0.02560.1956-0.00470.07829.537-1.8348-16.2416
30.9839-0.64580.19121.4581-0.40430.8650.03390.0396-0.1013-0.05740.00130.06120.0628-0.0243-0.03570.0838-0.0038-0.0040.0673-0.00880.0673-1.0252-4.8301-31.0613
40.6553-0.14020.00490.5124-0.39160.60570.0098-0.0165-0.05770.03140.02220.10140.0068-0.0313-0.03180.0662-0.00170.00410.0739-0.00320.0759-11.25377.432-25.1271
51.4657-0.60681.03532.1274-0.49690.73370.03280.15050.0593-0.2336-0.0277-0.03750.0171-0.012-0.0140.06620.00270.00630.05-0.00660.0501-2.07521.8065-44.5089
61.2752-0.71960.09511.54-0.40091.57050.14280.1496-0.0443-0.4059-0.06550.0720.1051-0.0018-0.03850.16060.0068-0.01940.0765-0.00930.0605-5.557211.3499-45.8645
71.1214-0.1174-0.18610.6274-0.38580.96930.09220.0587-0.0122-0.1213-0.0698-0.03090.03560.0423-0.02120.0820.0055-0.00010.0483-0.00740.04561.830916.7795-39.5839
80.6318-0.05360.2931.83-0.62591.81260.0031-0.1603-0.05940.2775-0.02340.00710.1283-0.05440.02390.1205-0.00070.00750.10240.00640.0659-2.0214-3.3965-14.5005
90.1716-0.045-0.09851.0659-0.84711.24620.0033-0.03360.02690.0461-0.0389-0.0451-0.09460.05940.03830.0747-0.0104-0.00320.0735-0.00570.07094.282820.1614-30.5523
102.20022.6448-1.02894.687-1.5620.878-0.05380.15440.0284-0.11030.1430.17030.0292-0.1655-0.08860.07470.0024-0.00510.10450.00560.0927-19.949617.3753-37.3029
112.2066-0.27010.40262.14020.02152.54940.0421-0.14790.1410.0362-0.01660.0163-0.0179-0.0406-0.00830.06270.00840.01960.07910.00790.078-17.389316.5269-22.3881
120.89650.001-0.140.9777-0.25750.9183-0.0003-0.0981-0.04890.1541-0.0268-0.14640.03720.07410.04720.0775-0.0015-0.01970.070.00990.074726.1666-2.597817.0112
130.7395-0.57170.18791.5046-0.42460.90590.00230.0225-0.0769-0.07260.02110.02510.0553-0.0286-0.02090.0679-0.0025-0.00260.0536-0.00650.060316.4612-5.65476.2517
141.00710.0109-0.00120.4176-0.26780.53280.02160.00070.00620.04760.01730.0856-0.012-0.0218-0.04210.0620.00510.01310.06470.00310.07036.20996.856112.9374
150.6364-0.13650.22851.3879-0.5550.8612-0.01360.09110.013-0.12270.05920.03870.0394-0.0729-0.03670.0548-0.01310.00110.07990.0120.061914.686413.832-6.125
160.21570.0813-0.08091.0605-0.53580.4386-0.0024-0.0350.01180.12760.0051-0.0058-0.0470.01670.00090.0570.0025-0.00270.0595-0.00360.051916.22514.519813.5695
170.3760.0259-0.19430.8026-0.6291.0270.0116-0.02650.06740.0745-0.0465-0.0718-0.06250.10580.0290.0524-0.0116-0.00240.0475-0.0010.066521.611519.09457.7059
181.8743.1218-0.99955.4916-1.85120.6477-0.04850.19350.1396-0.02110.21610.31810.0056-0.1249-0.16250.06050.01530.00390.12370.02920.1467-2.377816.98921.2124
194.04561.23941.14882.020.34652.0250.0427-0.21860.25330.1076-0.03810.1854-0.1248-0.11580.01790.07660.01120.0380.07730.0010.1076-0.090315.212115.7945
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 44 )A25 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 65 )A45 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 95 )A66 - 95
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 144 )A96 - 144
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 163 )A145 - 163
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 200 )A164 - 200
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 237 )A201 - 237
8X-RAY DIFFRACTION8chain 'A' and (resid 238 through 264 )A238 - 264
9X-RAY DIFFRACTION9chain 'A' and (resid 265 through 297 )A265 - 297
10X-RAY DIFFRACTION10chain 'A' and (resid 298 through 322 )A298 - 322
11X-RAY DIFFRACTION11chain 'A' and (resid 323 through 342 )A323 - 342
12X-RAY DIFFRACTION12chain 'B' and (resid 23 through 65 )B23 - 65
13X-RAY DIFFRACTION13chain 'B' and (resid 66 through 95 )B66 - 95
14X-RAY DIFFRACTION14chain 'B' and (resid 96 through 144 )B96 - 144
15X-RAY DIFFRACTION15chain 'B' and (resid 145 through 217 )B145 - 217
16X-RAY DIFFRACTION16chain 'B' and (resid 218 through 264 )B218 - 264
17X-RAY DIFFRACTION17chain 'B' and (resid 265 through 297 )B265 - 297
18X-RAY DIFFRACTION18chain 'B' and (resid 298 through 322 )B298 - 322
19X-RAY DIFFRACTION19chain 'B' and (resid 323 through 342 )B323 - 342

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