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- PDB-4n0q: Crystal Structure of an ABC transporter, substrate-binding protei... -

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Basic information

Entry
Database: PDB / ID: 4n0q
TitleCrystal Structure of an ABC transporter, substrate-binding protein from Brucella melitensis 16M in complex with L-Leucine using a crystal grown in a Crystal Former (Microlytic)
ComponentsLeu/Ile/Val-binding protein homolog 3
KeywordsTRANSPORT PROTEIN / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ABC transporter / amino-acid transport
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
Leu/Ile/Val-binding protein / 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
LEUCINE / Leu/Ile/Val-binding protein homolog 3
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of an ABC transporter, substrate-binding protein from Brucella melitensis 16M in complex with L-Leucine using a crystal grown in a Crystal Former (Microlytic)
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D.
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 20, 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: Leu/Ile/Val-binding protein homolog 3
B: Leu/Ile/Val-binding protein homolog 3
C: Leu/Ile/Val-binding protein homolog 3
D: Leu/Ile/Val-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,4268
Polymers146,9024
Non-polymers5254
Water8,953497
1
A: Leu/Ile/Val-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,7251
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leu/Ile/Val-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,7251
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leu/Ile/Val-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,7251
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Leu/Ile/Val-binding protein homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8572
Polymers36,7251
Non-polymers1311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.500, 59.850, 147.900
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Leu/Ile/Val-binding protein homolog 3


Mass: 36725.395 Da / Num. of mol.: 4 / Fragment: UNP residues 23-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI1930 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YEE8
#2: Chemical
ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
Crystal growTemperature: 294 K / Method: microfluidic / pH: 5.5
Details: SuperCOMBI(b4): 0.2 M magnesium chloride, 0.1 M Bis-Tris-HCl, pH 5.5, 25% PEG3350, MICROFLUIDIC, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 6, 2013
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 54462 / Num. obs: 53389 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.67
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.360.224.7183.3
2.36-2.420.2135.29195.4
2.42-2.490.1976.26199.8
2.49-2.570.1886.67199.9
2.57-2.660.1796.96199.8
2.66-2.750.1537.95199.7
2.75-2.850.139.29199.6
2.85-2.970.1269.47199.6
2.97-3.10.10810.71199.7
3.1-3.250.09112.57199.7
3.25-3.430.07814.64199.7
3.43-3.640.07116.29199.4
3.64-3.890.0619.21199.1
3.89-4.20.0619.15199.2
4.2-4.60.05122.08199.1
4.6-5.140.05220.11198.9
5.14-5.940.06515.68199.5
5.94-7.270.06615.67199.5
7.27-10.290.04123.99198.9
10.290.03624.33196

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å45.35 Å
Translation2.3 Å45.35 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IPC

3ipc


Resolution: 2.3→19.93 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.32 / SU B: 14.24 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26875 2727 5.1 %RANDOM
Rwork0.21226 ---
obs0.21518 50570 97.88 %-
all-56012 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0.18 Å2
2--0.49 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9698 0 36 497 10231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199913
X-RAY DIFFRACTIONr_bond_other_d0.0010.029377
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.95813501
X-RAY DIFFRACTIONr_angle_other_deg0.799321517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55651381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50125.955356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.337151452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3921520
X-RAY DIFFRACTIONr_chiral_restr0.0720.21606
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211652
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022044
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_it0.8591.1265527
X-RAY DIFFRACTIONr_mcbond_other0.8591.1265526
X-RAY DIFFRACTIONr_mcangle_it1.4321.6846898
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7921.1434386
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 148 -
Rwork0.246 3110 -
obs--83.3 %
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)
12.1069-0.65750.46050.28810.03320.4834-0.0131-0.1437-0.1157-0.06240.06150.0184-0.10790.0127-0.04840.3613-0.00480.22120.02530.01430.149149.348347.075169.1651
20.52090.4367-0.34911.75920.34860.53590.0342-0.06860.021-0.04470.0074-0.0866-0.02410.0685-0.04160.3111-0.01190.19120.0217-0.01010.120252.120857.03380.5144
30.58730.2195-0.00230.64030.00260.32160.04480.0240.0390.0448-0.06720.03590.00360.070.02250.15790.0143-0.06530.1420.01460.225650.203220.7531152.6811
40.2387-0.1361-0.18520.4548-0.02650.25940.0410.05310.0167-0.0421-0.02010.0143-0.0114-0.0418-0.02090.13420.0095-0.07130.1406-0.00210.239847.394530.7866141.403
50.4555-0.211-0.44572.06781.07790.9723-0.0849-0.03370.0041-0.17370.00060.1533-0.07030.0350.08430.20950.0370.07160.07650.02580.078930.419349.2369102.2711
60.0755-0.086-0.11991.26551.06631.4077-0.0388-0.08820.01150.1572-0.0305-0.06370.1210.05650.06920.19280.01540.06170.1243-0.00690.08133.398649.713114.0869
70.22940.0638-0.11590.8195-0.47060.5420.07790.0289-0.0003-0.0622-0.0714-0.0440.01470.0118-0.00650.17790.0451-0.03580.15640.02980.165268.687820.7057118.7329
80.73440.4914-0.25941.9629-0.61420.6113-0.01790.24020.0536-0.44360.08590.14020.0831-0.079-0.0680.24590.0596-0.01740.21650.07730.043264.747327.9136104.6577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 158
2X-RAY DIFFRACTION2A159 - 355
3X-RAY DIFFRACTION3B23 - 158
4X-RAY DIFFRACTION4B159 - 355
5X-RAY DIFFRACTION5C24 - 225
6X-RAY DIFFRACTION6C226 - 355
7X-RAY DIFFRACTION7D24 - 261
8X-RAY DIFFRACTION8D262 - 355

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