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- PDB-3n0x: Crystal structure of an ABC-type branched-chain amino acid transp... -

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Basic information

Entry
Database: PDB / ID: 3n0x
TitleCrystal structure of an ABC-type branched-chain amino acid transporter (RPA4397) from Rhodopseudomonas palustris CGA009 at 1.50 A resolution
ComponentsPossible substrate binding protein of ABC transporter system
KeywordsTRANSPORT PROTEIN / Receptor family ligand binding region / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
: / 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
Possible substrate binding protein of ABC transporter system
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an ABC-type branched-chain amino acid transporter (RPA4397) from Rhodopseudomonas palustris CGA009 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Possible substrate binding protein of ABC transporter system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5124
Polymers41,2351
Non-polymers2763
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.736, 41.806, 75.979
Angle α, β, γ (deg.)90.000, 110.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Possible substrate binding protein of ABC transporter system / ABC-type branched-chain amino acid transporter


Mass: 41235.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Gene: RPA4397 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6N1K8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 16-388) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 16-388) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.12 Å3/Da / Density % sol: 41.9 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2000M NaOAc, 30.0000% PEG-8000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97949,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 10, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (ho rizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.978981
ReflectionResolution: 1.5→29.348 Å / Num. obs: 55240 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.302 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.5-1.550.4411.718484964394.6
1.55-1.620.3252.3225191165696.4
1.62-1.690.251319198992796.7
1.69-1.780.194204961059096.9
1.78-1.890.1295.7201081038797
1.89-2.040.0789.1207891072096.8
2.04-2.240.05413.1198371023496.8
2.24-2.560.03917.5201501042096.8
2.56-3.230.02624206051067197.2
3.23-29.3480.01836.2202771049496.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.348 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.697 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM TLS GROUPS. 5. GLYCEROL (GOL) FROM THE CRYOPROTECTANT SOLUTION HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2800 5.1 %RANDOM
Rwork0.148 ---
obs0.149 55225 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.75 Å2 / Biso mean: 21.167 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20.02 Å2
2--1.5 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 18 526 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223070
X-RAY DIFFRACTIONr_bond_other_d0.0010.022085
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9744212
X-RAY DIFFRACTIONr_angle_other_deg0.91935157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.92125.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81115537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4361512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_mcbond_it1.21421942
X-RAY DIFFRACTIONr_mcbond_other0.2522784
X-RAY DIFFRACTIONr_mcangle_it2.12543158
X-RAY DIFFRACTIONr_scbond_it3.49461128
X-RAY DIFFRACTIONr_scangle_it5.21781023
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 195 -
Rwork0.243 3800 -
all-3995 -
obs--99.03 %
Refinement TLS params.Method: refined / Origin x: 26.8675 Å / Origin y: 8.6908 Å / Origin z: 53.8698 Å
111213212223313233
T0.0312 Å20.0055 Å2-0.0062 Å2-0.0031 Å20.0035 Å2--0.0194 Å2
L0.9112 °20.209 °2-0.1313 °2-0.301 °20.0379 °2--0.3413 °2
S0.0139 Å °-0.0508 Å °-0.0074 Å °-0.0011 Å °-0.0119 Å °0.0056 Å °-0.0243 Å °-0.0191 Å °-0.002 Å °

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