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- PDB-4q6b: Crystal Structure of ABC Transporter Substrate-Binding Protein fr... -

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Basic information

Entry
Database: PDB / ID: 4q6b
TitleCrystal Structure of ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense complex with Leu
ComponentsExtracellular ligand-binding receptor
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / SBP
Function / homology
Function and homology information


amino acid transport / metal ion binding
Similarity search - Function
Leu/Ile/Val-binding protein / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.667 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2014
Title: Crystal Structure of ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense complex with Leu
Authors: Kim, Y. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6357
Polymers39,2601
Non-polymers3766
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.425, 42.765, 63.577
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Extracellular ligand-binding receptor


Mass: 39259.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: Dhaf_0110 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: B8FZ96
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium chloride, 20 % PEG3350, pH 7.5, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 31, 2013 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.667→50 Å / Num. all: 35641 / Num. obs: 35641 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 18.93 Å2 / Rsym value: 0.126 / Net I/σ(I): 10
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1633 / Rsym value: 0.442 / % possible all: 92.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 4MLC

4mlc


Resolution: 1.667→31.092 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1784 5.01 %random
Rwork0.168 ---
all0.17 35607 --
obs0.17 35607 98.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.667→31.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 20 198 2811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142740
X-RAY DIFFRACTIONf_angle_d1.4813717
X-RAY DIFFRACTIONf_dihedral_angle_d14.439997
X-RAY DIFFRACTIONf_chiral_restr0.103395
X-RAY DIFFRACTIONf_plane_restr0.008500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.667-1.71210.24321170.21042210232784
1.7121-1.76250.22551310.20852554268598
1.7625-1.81940.24221500.191325972847100
1.8194-1.88440.26881280.19126262754100
1.8844-1.95980.22731220.177926502772100
1.9598-2.0490.24311530.1826182771100
2.049-2.1570.22491500.167926122762100
2.157-2.29210.19641350.167526172752100
2.2921-2.4690.18431480.168726502798100
2.469-2.71730.20681400.164926342774100
2.7173-3.11020.24111300.175126602790100
3.1102-3.91730.19291370.156426762813100
3.9173-31.09720.17041430.15432719286299
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)
12.81570.6540.31662.8463-0.02042.3705-0.01580.1192-0.0139-0.14490.0081-0.37-0.00550.165-0.01090.08490.00990.03290.1004-0.00580.120839.3539-5.986115.974
22.942-1.58370.98370.9039-0.46120.4127-0.0497-0.0797-0.00250.07740.0610.014-0.0247-0.0952-0.02230.1544-0.00840.01910.14530.00410.121421.651-5.358321.7003
31.64261.04291.2032.11111.06481.7787-0.07250.2544-0.0822-0.24150.10230.06910.13920.073-0.03390.21230.0161-0.03150.16310.00440.13867.27942.1067.0893
45.4143-0.1975-4.31266.27473.85737.6980.1750.0170.4683-0.39680.1148-0.5889-0.45970.3766-0.28230.1614-0.01140.00630.11080.04710.213536.543913.512112.3321
52.5091-1.02760.8922.3928-0.85211.489-0.1552-0.13320.19520.22780.08030.0321-0.231-0.16680.08240.137-0.00170.01830.1286-0.03390.125329.02253.687923.5564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 261 )
4X-RAY DIFFRACTION4chain 'A' and (resid 262 through 280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 281 through 351 )

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