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- PDB-4mlc: ABC Transporter Substrate-Binding Protein fromDesulfitobacterium ... -

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Basic information

Entry
Database: PDB / ID: 4mlc
TitleABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense
ComponentsExtracellular ligand-binding receptor
KeywordsSIGNALING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / SBP (substrate-binding protein) / alpha-beta-alpha sandwich
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
Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.705 Å
AuthorsKim, Y. / Chhor, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: ABC Transporter Substrate-Binding Protein fromDesulfitobacterium hafniense
Authors: Kim, Y. / Chhor, G. / Endres, M. / Joachimiak, A.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.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

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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)39,4924
Polymers39,2601
Non-polymers2323
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Extracellular ligand-binding receptor
hetero molecules

A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9838
Polymers78,5192
Non-polymers4646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area3240 Å2
ΔGint-74 kcal/mol
Surface area27290 Å2
MethodPISA
3
A: Extracellular ligand-binding receptor
hetero molecules

A: Extracellular ligand-binding receptor
hetero molecules

A: Extracellular ligand-binding receptor
hetero molecules

A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,96716
Polymers157,0384
Non-polymers92912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area9210 Å2
ΔGint-161 kcal/mol
Surface area51840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.195, 81.796, 128.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 magic / References: UniProt: B8FZ96
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Calciam Acetate, 0.1 M sodium Caccodylate pH 6.5, 40 % (v/v) PEG300, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 11736 / Num. obs: 11736 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 30.58 Å2 / Rsym value: 0.089 / Net I/σ(I): 15.1
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.35 / Num. unique all: 583 / Rsym value: 0.698 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.705→34.972 Å / SU ML: 0.3 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1130 9.98 %random
Rwork0.166 ---
all0.171 11328 --
obs0.171 11328 96.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.7 Å2
Refinement stepCycle: LAST / Resolution: 2.705→34.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 11 38 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012681
X-RAY DIFFRACTIONf_angle_d1.243635
X-RAY DIFFRACTIONf_dihedral_angle_d15.77964
X-RAY DIFFRACTIONf_chiral_restr0.088386
X-RAY DIFFRACTIONf_plane_restr0.005485
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7054-2.82850.29421240.19521041116581
2.8285-2.97750.25981250.19021227135294
2.9775-3.1640.24521380.1831274141297
3.164-3.40810.21411490.16821291144099
3.4081-3.75070.21811470.153313061453100
3.7507-4.29260.21511450.144113301475100
4.2926-5.4050.19811440.144713381482100
5.405-34.97490.19231580.18551391154999
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)
13.4508-0.4124-0.11442.81330.21182.5404-0.02470.17660.3209-0.0680.06670.3751-0.3213-0.18-0.0250.20350.0529-0.01320.22660.15410.277762.216323.265241.0293
20.44110.5742-0.16481.7849-0.00710.0776-0.0592-0.00750.0199-0.13770.0499-0.02120.05130.0156-0.03030.2025-0.01580.00810.19320.05310.138269.37999.885751.3269
32.33410.05320.07421.87450.6593.98270.12160.1535-0.1418-0.08660.03120.02640.13110.0302-0.14410.1683-0.071-0.04690.19140.00010.197367.212-13.591745.4107
42.2286-2.935-0.29136.1764-0.55051.3085-0.08890.1886-0.2532-0.0381-0.0360.8161-0.0383-0.20420.14240.1675-0.0554-0.06560.3330.0990.365747.97236.537945.3097
52.1640.68950.89735.06880.42362.27870.0212-0.26130.20220.551-0.0880.3705-0.1794-0.30650.07550.23460.0950.07180.30890.05860.170358.131914.178453.944
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 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 281 through 351 )

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