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- PDB-4edp: 1.85 Angstrom resolution crystal structure of an ABC transporter ... -

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Basic information

Entry
Database: PDB / ID: 4edp
Title1.85 Angstrom resolution crystal structure of an ABC transporter from Clostridium perfringens ATCC 13124
ComponentsABC transporter, substrate-binding proteinATP-binding cassette transporter
KeywordsTRANSPORT PROTEIN / ABC transporter / substrate-binding protein / Clostridium perfringens ATCC 13124 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


polyamine binding / polyamine transport / periplasmic space
Similarity search - Function
Spermidine/putrescine-binding periplasmic protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ABC transporter, substrate-binding protein / ABC transporter, substrate-binding protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.85 Angstrom resolution crystal structure of an ABC transporter from Clostridium perfringens ATCC 13124
Authors: Halavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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 / 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 / _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: ABC transporter, substrate-binding protein
B: ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,32615
Polymers76,6522
Non-polymers67313
Water12,214678
1
A: ABC transporter, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6337
Polymers38,3261
Non-polymers3076
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)38,6928
Polymers38,3261
Non-polymers3667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.318, 50.743, 143.774
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38326.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / Gene: CPF_1477 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q0TR20, UniProt: A0A0H2YTW6*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: crystallization condition: 2M NH4 Citrate pH 7.0,0.1MBis-Tris Propane. Paratone used for cryoprotection, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2012 / Details: Be-Lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 68597 / Num. obs: 68597 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.17
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3387 / % possible all: 99.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A99

1a99


Resolution: 1.85→29.1 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.62 / SU ML: 0.049 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 3475 5.1 %RANDOM
Rwork0.16279 ---
obs0.16426 65106 99.54 %-
all-65106 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.842 Å2
Baniso -1Baniso -2Baniso -3
1--5.83 Å20 Å26.78 Å2
2---2.71 Å20 Å2
3---8.54 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 40 678 5628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225437
X-RAY DIFFRACTIONr_bond_other_d0.0010.023544
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9597422
X-RAY DIFFRACTIONr_angle_other_deg0.86838841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8485716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.81727.48246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.78115980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.307154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02951
X-RAY DIFFRACTIONr_mcbond_it0.8681.53455
X-RAY DIFFRACTIONr_mcbond_other0.2781.51362
X-RAY DIFFRACTIONr_mcangle_it1.57425636
X-RAY DIFFRACTIONr_scbond_it2.72831982
X-RAY DIFFRACTIONr_scangle_it4.5684.51786
LS refinement shellResolution: 1.851→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 201 -
Rwork0.209 4579 -
obs-4579 95.11 %
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)
11.9129-0.1101-0.09774.5633-1.13812.16910.02640.67360.118-0.4776-0.06020.14380.0105-0.03850.03390.2241-0.0335-0.02170.35870.03190.036811.850852.909939.3599
22.0514-0.1369-0.2941.32420.13741.4779-0.07450.2145-0.1211-0.1180.0355-0.01650.12270.12060.03910.0822-0.0010.00530.1159-0.00580.023518.046445.869253.3587
31.16320.16470.04951.5456-0.42041.09920.0305-0.003-0.02780.0140.04160.14810.0276-0.0305-0.07210.0426-0.0007-0.02050.0046-0.00420.0554-6.468637.814868.8427
43.3844-0.05211.08711.3694-0.23921.49260.0180.0972-0.2542-0.11730.02560.00250.06310.0924-0.04360.10020.0059-0.01170.0158-0.02060.0485-0.369831.720568.4714
52.11650.5187-0.41030.7622-0.37240.7607-0.0670.33220.0981-0.13130.08060.0823-0.0051-0.0165-0.01370.0923-0.0037-0.02980.07910.00180.03263.534250.091655.5333
61.6097-0.0531-0.11642.2501-0.57411.56060.03030.0997-0.0116-0.1025-0.05750.09930.0726-0.01810.02720.062-0.0001-0.02210.1032-0.02220.05254.45242.256563.2905
72.2850.0671-0.28593.95820.92582.6831-0.0077-0.50180.07430.3772-0.0392-0.1955-0.0140.06920.04690.1950.0305-0.01910.3205-0.03130.037633.437429.173631.4931
82.0618-0.0838-0.06481.4015-0.04681.6994-0.0686-0.2115-0.12980.09030.02320.0830.1695-0.17320.04540.0839-0.00650.0130.11820.00480.033827.182422.04717.7253
91.3172-0.30940.14041.55650.46491.13130.0140.0064-0.0425-0.02390.0454-0.1320.03390.0518-0.05940.0466-0.0025-0.01670.00430.00230.051651.787113.77342.2444
103.25880.01831.28231.40820.11281.66270.0101-0.0978-0.28310.11080.04110.01990.0364-0.1173-0.05130.0864-0.0048-0.00880.0180.01610.043444.99057.36081.995
112.1358-0.4265-0.51770.66040.37960.8458-0.0538-0.31560.08170.1130.0728-0.07860.00620.0056-0.01890.08830.0031-0.03310.0753-0.00240.028242.187325.915815.4529
121.723-0.0308-0.11381.97520.43381.4250.0502-0.10180.00550.1016-0.0882-0.10440.07050.03410.03790.0667-0.0049-0.01880.11010.01960.046140.849418.27277.7027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 65
2X-RAY DIFFRACTION2A66 - 134
3X-RAY DIFFRACTION3A135 - 183
4X-RAY DIFFRACTION4A184 - 221
5X-RAY DIFFRACTION5A222 - 304
6X-RAY DIFFRACTION6A305 - 348
7X-RAY DIFFRACTION7B33 - 65
8X-RAY DIFFRACTION8B66 - 134
9X-RAY DIFFRACTION9B135 - 183
10X-RAY DIFFRACTION10B184 - 219
11X-RAY DIFFRACTION11B220 - 304
12X-RAY DIFFRACTION12B305 - 348

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