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- PDB-4pyr: Structure of a putative branched-chain amino acid ABC transporter... -

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Basic information

Entry
Database: PDB / ID: 4pyr
TitleStructure of a putative branched-chain amino acid ABC transporter from Chromobacterium violaceum ATCC 12472
ComponentsPutative branched-chain amino acid ABC transporter
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Amino acid transporter
Function / homology
Function and homology information


periplasmic side of cell outer membrane / peptidoglycan biosynthetic process / enzyme regulator activity
Similarity search - Function
Penicillin-binding protein activator LpoA / LppC putative lipoprotein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Penicillin-binding protein activator
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a putative branched-chain amino acid ABC transporter from Chromobacterium violaceum ATCC 12472
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Mar 26, 2025Group: 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 / 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_leaving_atom_flag / _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: Putative branched-chain amino acid ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6062
Polymers32,2991
Non-polymers3071
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.182, 72.332, 45.146
Angle α, β, γ (deg.)90.00, 95.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative branched-chain amino acid ABC transporter


Mass: 32298.789 Da / Num. of mol.: 1 / Fragment: UNP residues 83-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV_0653 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 magic / References: UniProt: Q7P0B4
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2014 / Details: MIRROR
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 46422 / Num. obs: 46422 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 34.3
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.926 / SU ML: 0.071 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23289 2347 5.1 %RANDOM
Rwork0.18565 ---
obs0.18793 44047 99.36 %-
all-44047 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.384 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å2-0 Å2-0.49 Å2
2--2.93 Å2-0 Å2
3----0.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 20 220 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192339
X-RAY DIFFRACTIONr_bond_other_d0.0010.022307
X-RAY DIFFRACTIONr_angle_refined_deg1.7232.0013189
X-RAY DIFFRACTIONr_angle_other_deg0.84235278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1515315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78522.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19815349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0791526
X-RAY DIFFRACTIONr_chiral_restr0.0970.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02518
X-RAY DIFFRACTIONr_mcbond_it2.4841.0621239
X-RAY DIFFRACTIONr_mcbond_other2.4767.9461237
X-RAY DIFFRACTIONr_mcangle_it2.8291.6081561
X-RAY DIFFRACTIONr_mcangle_other2.8281562
X-RAY DIFFRACTIONr_scbond_it3.2151100
X-RAY DIFFRACTIONr_scbond_other3.2031099
X-RAY DIFFRACTIONr_scangle_other3.5731628
X-RAY DIFFRACTIONr_long_range_B_refined3.6692776
X-RAY DIFFRACTIONr_long_range_B_other3.5312700
X-RAY DIFFRACTIONr_rigid_bond_restr36.3532316
X-RAY DIFFRACTIONr_sphericity_bonded9.56752274
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 181 -
Rwork0.266 3130 -
obs--96.9 %
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)
14.46360.53891.22011.84330.22824.82210.02320.06690.0143-0.08390.0063-0.27950.07380.2003-0.02950.08390.005-0.00220.00850.00030.0939.610321.9284-1.8245
26.005-0.1089-0.16352.5327-0.17373.4825-0.0561-0.39550.59670.05220.1108-0.3893-0.16510.5043-0.05470.1347-0.0026-0.03460.1056-0.07720.211244.620731.04094.0525
36.61465.46790.23869.0678-1.00232.61960.4107-1.04760.52220.8426-0.3265-0.2873-0.22010.1098-0.08420.25090.02220.00870.2802-0.17820.269535.923634.063811.8232
42.9566-0.00360.52473.3838-0.32863.0221-0.0782-0.0562-0.16140.1721-0.01810.11840.098-0.1180.09630.1522-0.00010.00020.0060.00160.064516.886614.487723.6677
53.45071.2148-0.79281.81980.11562.8679-0.0715-0.0337-0.19960.16320.01010.06320.1573-0.26330.06130.11930.0169-0.00240.06260.0210.04727.262618.04460.2999
64.18371.8488-1.2043.99690.80541.90440.1458-0.04830.60870.18110.0160.0501-0.3075-0.0384-0.16190.1850.0544-0.02760.06960.00370.127123.77529.19595.9796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 118
2X-RAY DIFFRACTION2A119 - 169
3X-RAY DIFFRACTION3A170 - 186
4X-RAY DIFFRACTION4A187 - 302
5X-RAY DIFFRACTION5A303 - 348
6X-RAY DIFFRACTION6A349 - 381

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