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- PDB-4wed: Crystal structure of ABC transporter substrate-binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4wed
TitleCrystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti
ComponentsABC transporter, periplasmic solute-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter substrate-binding protein / Sinorhizobium meliloti / Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


nickel cation transport / nickel cation binding / ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / heme binding
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / ABC transporter, periplasmic solute-binding protein
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsShabalin, I.G. / Otwinowski, Z. / Bacal, P. / Cymborowski, M.T. / Handing, K.B. / Stead, M. / Hammonds, J. / Ahmed, M. / Bonanno, J. / Seidel, R. ...Shabalin, I.G. / Otwinowski, Z. / Bacal, P. / Cymborowski, M.T. / Handing, K.B. / Stead, M. / Hammonds, J. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: to be published
Title: Crystal structure of ABC transporter substrate-binding protein from Sinorhizobium meliloti
Authors: Shabalin, I.G. / Handing, K.B. / Minor, W.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, periplasmic solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1884
Polymers58,0271
Non-polymers1613
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-11 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.327, 57.327, 132.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein ABC transporter, periplasmic solute-binding protein


Mass: 58027.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: SMa1651 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92YH7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThere was an additional tag present in the crystallization setup, but it was likely cleaved by the ...There was an additional tag present in the crystallization setup, but it was likely cleaved by the chymotrypsin present. The sequence was MHHHHHHSSGVDLGTENLYFQS

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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: 43.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition # 18 (0.2 M Sodium Formate, 20% ...Details: 0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition # 18 (0.2 M Sodium Formate, 20% (w/v) PEG 3350 ) and equilibrated against 2.0 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07819 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2013 / Details: Bimorph K-B pair
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07819 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 19751 / % possible obs: 97.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Rrim(I) all: 0.065 / Χ2: 1.175 / Net I/av σ(I): 24.51 / Net I/σ(I): 15.6 / Num. measured all: 86540
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.60.7777940.6620.470.9130.8974.3
2.39-2.433.80.6388540.6950.3820.7480.96485.8
2.43-2.483.90.5199850.8210.2990.6020.94996.3
2.48-2.534.50.4589710.8830.2410.5180.96799.1
2.53-2.594.50.36810310.9160.1940.4170.97399.2
2.59-2.654.50.31510080.9520.1660.3560.97299.4
2.65-2.714.50.27110210.9560.1420.3061.02899.6
2.71-2.794.50.219740.9750.1110.2381.11299.6
2.79-2.874.50.16910450.9790.0890.1911.20199.3
2.87-2.964.60.149730.9870.0740.1581.2899.6
2.96-3.074.50.11510140.9890.0610.131.31599.5
3.07-3.194.50.09610370.9920.0510.1091.45199.7
3.19-3.334.50.089870.9940.0420.091.48999.8
3.33-3.514.50.06810100.9950.0360.0771.41399.8
3.51-3.734.50.05810000.9960.0310.0651.36899.8
3.73-4.024.40.05210200.9970.0280.0591.30599.6
4.02-4.424.40.04610120.9970.0250.0531.20799.7
4.42-5.064.40.0459960.9970.0240.0521.19199.8
5.06-6.374.30.04310250.9970.0230.0491.09100
6.37-504.20.0389940.9980.0210.0431.08497.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Blu-Icedata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
DMphasing
MLPHAREphasing
SHELXphasing
PDB_EXTRACT3.15data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→49.65 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.1741 / FOM work R set: 0.8026 / SU B: 18.319 / SU ML: 0.21 / SU R Cruickshank DPI: 0.383 / SU Rfree: 0.2455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 899 4.6 %RANDOM
Rwork0.1641 18838 --
obs0.1667 -97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 132.22 Å2 / Biso mean: 72.611 Å2 / Biso min: 43.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2.35→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 10 101 3720
Biso mean--65.35 66.62 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193712
X-RAY DIFFRACTIONr_bond_other_d0.0030.023413
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.9615076
X-RAY DIFFRACTIONr_angle_other_deg0.82437828
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37924.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45715500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.541516
X-RAY DIFFRACTIONr_chiral_restr0.0820.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02822
X-RAY DIFFRACTIONr_mcbond_it2.553.8111930
X-RAY DIFFRACTIONr_mcbond_other2.5513.8131931
X-RAY DIFFRACTIONr_mcangle_it3.725.7162409
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 65 -
Rwork0.25 1124 -
all-1189 -
obs--77.11 %
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)
12.5194-0.8062-0.32033.5319-0.36922.3857-0.19570.0647-0.23470.3127-0.1008-0.43030.26020.34330.29640.1221-0.0204-0.07920.11080.05270.5059-0.7810.746-5.177
22.65230.1505-2.582212.25930.0686.3294-0.16960.60950.43350.16610.3028-1.69240.08680.8718-0.13320.0479-0.0855-0.16680.71710.2580.964811.10915.394-9.022
33.0617-0.11080.06666.32710.92454.16930.06220.21110.7274-0.0137-0.3202-0.9155-0.45950.52560.2580.1434-0.1642-0.13340.23640.23290.7443.09623.864-9.653
45.10281.6616-2.16832.8193-2.53454.04530.26640.13150.8830.4064-0.1239-0.2223-0.8228-0.0605-0.14250.4195-0.0484-0.12450.05740.06220.7003-11.39629.674-2.975
57.0323-0.9854-1.7747.2308-2.44384.2754-0.1564-0.5482-0.22560.17280.12560.55070.2457-0.09590.03090.23140.1293-0.12070.2249-0.08310.3603-34.60419.89315.712
63.3215-0.841-1.15996.79581.33032.21380.07580.11540.0502-0.0877-0.0708-0.1384-0.5441-0.1345-0.00490.28880.0261-0.16090.09550.01280.377-22.43722.662-0.339
72.7035-1.1462-2.38230.8031.40716.7926-0.00210.02370.2247-0.0349-0.01040.04920.0483-0.48910.01260.17450.0375-0.15060.1546-0.08480.4408-39.63126.69414.424
810.31280.14211.94972.26660.99136.7044-0.0391-0.2243-0.18860.14290.2483-0.3099-0.09921.0905-0.20930.12230.0366-0.1250.3209-0.16460.4349-23.09828.53617.476
95.3048-1.85910.60284.46590.65450.2746-0.3235-0.4636-0.12320.29420.25560.111-0.0203-0.03960.06790.28650.0344-0.13840.19810.02410.4992-19.52911.2549.649
106.5064-1.59891.40546.189-0.04524.8867-0.3306-0.4809-1.17110.27390.1770.3309-0.04670.03980.15360.251-0.08820.00850.11050.06270.6011-25.0062.9328.59
113.2731-0.3315-1.52910.7777-0.12363.42-0.01410.0430.02710.1411-0.2085-0.0807-0.3041-0.25890.22260.1602-0.0009-0.15520.0954-0.00060.5086-21.82717.58-1.462
124.2157-0.5649-3.10662.5204-3.58469.16720.14960.35220.6090.1981-0.2553-0.3834-0.50950.22930.10580.2106-0.1593-0.1110.26550.11280.6052-3.90920.287-12.503
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 184
2X-RAY DIFFRACTION2A185 - 206
3X-RAY DIFFRACTION3A207 - 247
4X-RAY DIFFRACTION4A248 - 277
5X-RAY DIFFRACTION5A278 - 301
6X-RAY DIFFRACTION6A302 - 330
7X-RAY DIFFRACTION7A331 - 367
8X-RAY DIFFRACTION8A368 - 414
9X-RAY DIFFRACTION9A415 - 441
10X-RAY DIFFRACTION10A442 - 472
11X-RAY DIFFRACTION11A473 - 506
12X-RAY DIFFRACTION12A507 - 525

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