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

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Basic information

Entry
Database: PDB / ID: 4qym
TitleThe crystal structure of a solute-binding protein (N280D mutant) from Anabaena variabilis ATCC 29413 in complex with methionine
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
METHIONINE / VALINE / Amino acid/amide ABC transporter substrate-binding protein, HAAT family
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.581 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 methionine
Authors: Tan, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJul 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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 / 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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)85,3108
Polymers84,7292
Non-polymers5816
Water11,692649
1
A: Amino acid/amide ABC transporter substrate-binding protein, HAAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6554
Polymers42,3641
Non-polymers2913
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)42,6554
Polymers42,3641
Non-polymers2913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.964, 97.555, 150.151
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-741-

HOH

21A-784-

HOH

31A-818-

HOH

41B-822-

HOH

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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 ATCC 29413 (bacteria)
Strain: ATCC 29413 / PCC 7937 / Gene: Ava_0465 / References: UniProt: Q3MFZ5
#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-VAL / VALINE / Valine


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M MgCl, 0.1M Bis-Tris:HCl, 25%(w/v) PEG3350, 10mM Valine, Soaking condition - 0.2M MgCl, 0.1M Bis-Tris:HCl, 25%(w/v) PEG3350, 10mM Methionine, pH 6.5, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.58→25.63 Å / Num. all: 100412 / Num. obs: 100412 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 5.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 39.8
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.86 / % possible all: 93.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NV3

4nv3


Resolution: 1.581→25.629 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 5004 4.99 %
Rwork0.1683 --
obs0.1705 100332 99.3 %
all-100332 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.581→25.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 36 649 6108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065567
X-RAY DIFFRACTIONf_angle_d1.0247569
X-RAY DIFFRACTIONf_dihedral_angle_d13.3212020
X-RAY DIFFRACTIONf_chiral_restr0.067897
X-RAY DIFFRACTIONf_plane_restr0.005998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.581-1.59910.24191490.18752869X-RAY DIFFRACTION90
1.5991-1.61790.25241400.17763017X-RAY DIFFRACTION96
1.6179-1.63760.23331640.1783135X-RAY DIFFRACTION98
1.6376-1.65840.24881540.16863197X-RAY DIFFRACTION100
1.6584-1.68020.21971640.15723132X-RAY DIFFRACTION100
1.6802-1.70320.25961670.16043163X-RAY DIFFRACTION100
1.7032-1.72750.23781540.16153185X-RAY DIFFRACTION100
1.7275-1.75330.23391960.16933170X-RAY DIFFRACTION100
1.7533-1.78070.25531720.17193152X-RAY DIFFRACTION100
1.7807-1.80990.21161620.15733208X-RAY DIFFRACTION100
1.8099-1.84110.2431690.15263167X-RAY DIFFRACTION100
1.8411-1.87450.21281570.14723161X-RAY DIFFRACTION100
1.8745-1.91060.21271600.14453191X-RAY DIFFRACTION100
1.9106-1.94960.20571840.14123191X-RAY DIFFRACTION100
1.9496-1.99190.2051630.14283159X-RAY DIFFRACTION100
1.9919-2.03830.21251640.15433183X-RAY DIFFRACTION100
2.0383-2.08920.21221750.1473159X-RAY DIFFRACTION100
2.0892-2.14570.19691640.14643213X-RAY DIFFRACTION100
2.1457-2.20880.17811660.14623220X-RAY DIFFRACTION100
2.2088-2.280.19221370.14623194X-RAY DIFFRACTION100
2.28-2.36150.19041660.14533195X-RAY DIFFRACTION100
2.3615-2.45590.20121790.15343198X-RAY DIFFRACTION100
2.4559-2.56760.22191710.16713214X-RAY DIFFRACTION100
2.5676-2.70280.23111840.17173196X-RAY DIFFRACTION100
2.7028-2.8720.21221750.17673189X-RAY DIFFRACTION100
2.872-3.09340.2221750.18253212X-RAY DIFFRACTION100
3.0934-3.4040.21071630.18313235X-RAY DIFFRACTION100
3.404-3.89510.21432020.17853236X-RAY DIFFRACTION100
3.8951-4.90180.17341420.16713299X-RAY DIFFRACTION100
4.9018-25.63270.22951860.19893288X-RAY DIFFRACTION97

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