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- PDB-4nv3: The crystal structure of a solute-binding protein (N280D mutant) ... -

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Basic information

Entry
Database: PDB / ID: 4nv3
TitleThe crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with valine.
ComponentsAmino acid/amide ABC transporter substrate-binding protein, HAAT family
KeywordsTRANSPORT PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / VALINE / Amino acid/amide ABC transporter substrate-binding protein, HAAT family
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsTan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with valine.
Authors: Tan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
B: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0717
Polymers84,7292
Non-polymers3425
Water18,5551030
1
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5654
Polymers42,3641
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5063
Polymers42,3641
Non-polymers1412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.869, 100.932, 150.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

21A-947-

HOH

31B-938-

HOH

DetailsExperimentally unknown. It is predicted to be monomeric.

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Components

#1: Protein Amino acid/amide ABC transporter substrate-binding protein, HAAT family


Mass: 42364.367 Da / Num. of mol.: 2 / Mutation: N280D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: Anabaena variabilis, Ava_0465SG / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q3MFZ5
#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1030 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium Citrate:HCl, 20% (v/v)2-Propanol, 20% (w/v) PEG4000, 10mM Valine., pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97883 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.09→19.2 Å / Num. all: 308341 / Num. obs: 308341 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.7 % / Biso Wilson estimate: 8.07 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.9
Reflection shellResolution: 1.09→1.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 1.89 / Num. unique all: 9118 / % possible all: 88.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NOR

4nor
PDB Unreleased entry


Resolution: 1.09→19.117 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 12.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1428 15562 5.05 %random
Rwork0.1279 ---
all0.1286 308255 --
obs0.1286 308255 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.09→19.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 22 1030 6536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055947
X-RAY DIFFRACTIONf_angle_d1.1468142
X-RAY DIFFRACTIONf_dihedral_angle_d12.942293
X-RAY DIFFRACTIONf_chiral_restr0.08950
X-RAY DIFFRACTIONf_plane_restr0.0061088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0897-1.10210.23184910.22838507X-RAY DIFFRACTION88
1.1021-1.1150.22735130.20149316X-RAY DIFFRACTION96
1.115-1.12860.21175020.18549604X-RAY DIFFRACTION98
1.1286-1.14290.17745090.16849712X-RAY DIFFRACTION99
1.1429-1.15790.16965180.15559783X-RAY DIFFRACTION100
1.1579-1.17380.17635020.15119759X-RAY DIFFRACTION100
1.1738-1.19060.16635130.14529753X-RAY DIFFRACTION100
1.1906-1.20830.16174900.13789789X-RAY DIFFRACTION100
1.2083-1.22720.1465180.13169749X-RAY DIFFRACTION100
1.2272-1.24730.14335410.12439767X-RAY DIFFRACTION100
1.2473-1.26880.13485060.12079790X-RAY DIFFRACTION100
1.2688-1.29190.13615230.11789762X-RAY DIFFRACTION100
1.2919-1.31670.13965060.11579797X-RAY DIFFRACTION100
1.3167-1.34360.1425290.11819771X-RAY DIFFRACTION100
1.3436-1.37280.13975150.1169838X-RAY DIFFRACTION100
1.3728-1.40470.13015240.11199765X-RAY DIFFRACTION100
1.4047-1.43990.12935670.10889768X-RAY DIFFRACTION100
1.4399-1.47880.12765430.10789751X-RAY DIFFRACTION100
1.4788-1.52230.12515350.10289799X-RAY DIFFRACTION100
1.5223-1.57140.12445080.10469836X-RAY DIFFRACTION100
1.5714-1.62750.13345320.10949789X-RAY DIFFRACTION100
1.6275-1.69260.12554770.11189871X-RAY DIFFRACTION100
1.6926-1.76960.13245510.11819841X-RAY DIFFRACTION100
1.7696-1.86290.13575210.12439824X-RAY DIFFRACTION100
1.8629-1.97950.13324910.1269890X-RAY DIFFRACTION100
1.9795-2.13210.13915290.12449875X-RAY DIFFRACTION100
2.1321-2.34630.14145240.12779905X-RAY DIFFRACTION100
2.3463-2.6850.1474850.13679955X-RAY DIFFRACTION100
2.685-3.37980.14865350.139610002X-RAY DIFFRACTION100
3.3798-19.11960.14055640.126310125X-RAY DIFFRACTION99

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