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- PDB-3c9h: Crystal structure of the substrate binding protein of the ABC tra... -

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Basic information

Entry
Database: PDB / ID: 3c9h
TitleCrystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens
ComponentsABC transporter, substrate binding proteinATP-binding cassette transporter
KeywordsTRANSPORT PROTEIN / substrate binding protein / ABC transporter / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / periplasmic space / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / ABC transporter, substrate binding protein (Iron)
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the substrate binding protein of the ABC transporter from Agrobacterium tumefaciens.
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, substrate binding protein
B: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3636
Polymers78,9302
Non-polymers4334
Water7,800433
1
A: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6813
Polymers39,4651
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6813
Polymers39,4651
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.313, 86.947, 109.642
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABC transporter, substrate binding protein / ATP-binding cassette transporter


Mass: 39465.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: GI:17936349, AGR_C_4480, Atu2467 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7CWZ6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium citrate, 0.2M Ammonium acetate, 30% PEG 4000, 10mM ATP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2006 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→68.2 Å / Num. all: 54496 / Num. obs: 54136 / % possible obs: 99.34 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 19.78
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 1.57 / Num. unique all: 4178 / % possible all: 97.77

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→35.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.333 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.497 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22817 2898 5.1 %RANDOM
Rwork0.17259 ---
all0.17539 54136 --
obs0.17539 54136 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--1.49 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 28 433 5726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225415
X-RAY DIFFRACTIONr_bond_other_d0.0010.023672
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9567356
X-RAY DIFFRACTIONr_angle_other_deg0.93438897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94623.306245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92115871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9771542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
X-RAY DIFFRACTIONr_nbd_refined0.2180.21185
X-RAY DIFFRACTIONr_nbd_other0.1980.23819
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22594
X-RAY DIFFRACTIONr_nbtor_other0.0860.22743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2376
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.219
X-RAY DIFFRACTIONr_mcbond_it1.4861.54314
X-RAY DIFFRACTIONr_mcbond_other0.5441.51351
X-RAY DIFFRACTIONr_mcangle_it1.72625399
X-RAY DIFFRACTIONr_scbond_it3.03332439
X-RAY DIFFRACTIONr_scangle_it4.114.51957
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 206 -
Rwork0.235 3879 -
obs-4085 97.77 %
Refinement TLS params.Method: refined / Origin x: 37.753 Å / Origin y: -0.084 Å / Origin z: 11.145 Å
111213212223313233
T-0.0293 Å20.0063 Å2-0.0003 Å2--0.0228 Å20.0024 Å2---0.0462 Å2
L0.6245 °20.1767 °2-0.0115 °2-0.1016 °2-0.0221 °2--0.2935 °2
S0.0131 Å °0.0196 Å °0.0044 Å °-0.0151 Å °0.0184 Å °-0.0024 Å °-0.0121 Å °-0.0162 Å °-0.0314 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 6016 - 60
2X-RAY DIFFRACTION1AA61 - 10061 - 100
3X-RAY DIFFRACTION1AA101 - 150101 - 150
4X-RAY DIFFRACTION1AA151 - 200151 - 200
5X-RAY DIFFRACTION1AA201 - 250201 - 250
6X-RAY DIFFRACTION1AA251 - 300251 - 300
7X-RAY DIFFRACTION1AA301 - 354301 - 354
8X-RAY DIFFRACTION1BB15 - 6015 - 60
9X-RAY DIFFRACTION1BB61 - 10061 - 100
10X-RAY DIFFRACTION1BB101 - 150101 - 150
11X-RAY DIFFRACTION1BB151 - 200151 - 200
12X-RAY DIFFRACTION1BB201 - 250201 - 250
13X-RAY DIFFRACTION1BB251 - 300251 - 300
14X-RAY DIFFRACTION1BB301 - 353301 - 353

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