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- PDB-4gvo: Putative L-Cystine ABC transporter from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 4gvo
TitlePutative L-Cystine ABC transporter from Listeria monocytogenes
ComponentsLmo2349 protein
KeywordsTRANSPORT PROTEIN / structural genomics / IDP05245 / L-Cystine / ABC transporter / periplasmic binding protein / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-OXY CYSTEINE / HISTIDINE / Lmo2349 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.448 Å
AuthorsOsipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Putative L-Cystine ABC transporter from Listeria monocytogenes
Authors: Osipiuk, J. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_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.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_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: Lmo2349 protein
B: Lmo2349 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,45810
Polymers53,7552
Non-polymers7048
Water14,664814
1
A: Lmo2349 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2295
Polymers26,8771
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lmo2349 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2295
Polymers26,8771
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.990, 170.628, 45.049
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lmo2349 protein


Mass: 26877.311 Da / Num. of mol.: 2 / Mutation: 30-269 fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: strain ATCC BAA-679 / EGD-e / Gene: lmo2349 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y4T3

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Non-polymers , 5 types, 822 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N3O2
#5: Chemical ChemComp-CSX / S-OXY CYSTEINE


Type: L-peptide linking / Mass: 137.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 45.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium chloride, 20% PEG-3350, 0.01 M histidine , 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.448→31.8 Å / Num. all: 76793 / Num. obs: 76793 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.7
Reflection shellResolution: 1.448→1.48 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4.31 / Num. unique all: 2140 / % possible all: 51.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
HKL-3000phasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O1M

2o1m


Resolution: 1.448→31.8 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.733 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.065 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15355 3796 4.9 %RANDOM
Rwork0.1061 ---
all0.10841 72947 --
obs0.10841 72947 90.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.2 Å2
2---0.26 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.448→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 42 814 4536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024084
X-RAY DIFFRACTIONr_bond_other_d0.0010.022840
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9795556
X-RAY DIFFRACTIONr_angle_other_deg0.93837096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60226.72189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5415838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.322159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr3.39836924
X-RAY DIFFRACTIONr_sphericity_free29.3935167
X-RAY DIFFRACTIONr_sphericity_bonded9.43757477
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 152 -
Rwork0.164 3049 -
obs-3201 51.63 %

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