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- PDB-3n0w: Crystal structure of a branched chain amino acid ABC transporter ... -

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Basic information

Entry
Database: PDB / ID: 3n0w
TitleCrystal structure of a branched chain amino acid ABC transporter periplasmic ligand-binding protein (Bxe_C0949) from BURKHOLDERIA XENOVORANS LB400 at 1.88 A resolution
ComponentsABC branched chain amino acid family transporter, periplasmic ligand binding protein
KeywordsTRANSPORT PROTEIN / Receptor family ligand binding region / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLeucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICKEL (II) ION / Amino acid/amide ABC transporter substrate-binding protein, HAAT family
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a branched chain amino acid ABC transporter periplasmic ligand-binding protein (Bxe_C0949) from BURKHOLDERIA XENOVORANS LB400 at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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_asym_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.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_conn.ptnr2_label_seq_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: ABC branched chain amino acid family transporter, periplasmic ligand binding protein
B: ABC branched chain amino acid family transporter, periplasmic ligand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0313
Polymers82,9732
Non-polymers591
Water13,133729
1
A: ABC branched chain amino acid family transporter, periplasmic ligand binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5452
Polymers41,4861
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABC branched chain amino acid family transporter, periplasmic ligand binding protein


Theoretical massNumber of molelcules
Total (without water)41,4861
Polymers41,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.545, 58.269, 145.338
Angle α, β, γ (deg.)90.000, 98.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A26 - 399
2114B26 - 399
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein ABC branched chain amino acid family transporter, periplasmic ligand binding protein


Mass: 41486.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_C0896, Bxe_C0949 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13GG5
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT 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. THE CLONED CONSTRUCT CONTAINS RESIDUES 22-399 OF THE FULL LENGTH PROTEIN.

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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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.86
Details: 14.0000% polyethylene glycol monomethyl ether 2000, 0.0100M nickel (II) chloride, 0.1M TRIS pH 8.86, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97915,0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 24, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979151
30.978981
ReflectionResolution: 1.88→29.134 Å / Num. obs: 62570 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.278 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.93
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.970.5581.411456766457.3
1.97-2.050.4231.7182961252696.8
2.05-2.140.2882.4177181211497.4
2.14-2.250.2263.1179451224997.4
2.25-2.390.1793.9183071246097.1
2.39-2.580.1315.2191071290497.1
2.58-2.840.0936.9183891245296.3
2.84-3.250.069.9182141222895.5
3.25-4.080.0414.5176831189693.2
4.08-29.1340.0318.9180701199292.2

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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: 1.88→29.134 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 7.021 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.151
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A NICKEL ION FROM THE CRYSTALLIZATION SOLUTION IS MODELED IN THE STRUCTURE. THE PRESENCE OF NICKEL (NI) AT THIS SITE IS SUPPORTED BY BINDING GEOMETRY, ANOMALOUS DIFFERENCE FOURIERS, ELECTRON DENSITY PEAK HEIGHT AND X-RAY FLUORESCENCE. 5. THERE IS SOME UNMODELED ELECTRON DENSITY NEAR RESIDUE 129 IN EACH SUBSUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3167 5.1 %RANDOM
Rwork0.191 ---
obs0.193 62555 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.78 Å2 / Biso mean: 28.782 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20.19 Å2
2---0.79 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.88→29.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 1 729 6367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226018
X-RAY DIFFRACTIONr_bond_other_d0.0010.024019
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9548176
X-RAY DIFFRACTIONr_angle_other_deg1.44339835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09524.606254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2561532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026983
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021241
X-RAY DIFFRACTIONr_mcbond_it0.7491.53865
X-RAY DIFFRACTIONr_mcbond_other0.1641.51608
X-RAY DIFFRACTIONr_mcangle_it1.29126186
X-RAY DIFFRACTIONr_scbond_it2.19432153
X-RAY DIFFRACTIONr_scangle_it3.344.51990
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4572 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.290.5
MEDIUM THERMAL0.672
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 149 -
Rwork0.297 2537 -
all-2686 -
obs--56.33 %
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)
10.74410.239-0.15560.8084-0.06180.72610.004200.0561-0.0424-0.0080.0171-0.03220.00930.00380.00910.009-0.00750.1084-0.00610.0945-9.09626.604129.763
20.7802-0.2920.61541.11-0.56532.06550.1130.0726-0.0821-0.2533-0.0422-0.02880.21090.1963-0.07090.25860.030.020.162-0.02440.1191-2.50225.55189.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 399
2X-RAY DIFFRACTION2B26 - 399

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