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- PDB-3n5l: Crystal structure of a binding protein component of ABC phosphona... -

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Basic information

Entry
Database: PDB / ID: 3n5l
TitleCrystal structure of a binding protein component of ABC phosphonate transporter (PA3383) from Pseudomonas aeruginosa at 1.97 A resolution
ComponentsBinding protein component of ABC phosphonate transporter
KeywordsTRANSPORT PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / ABC transport system / periplasmic phosphonate-binding
Function / homology
Function and homology information


organic phosphonate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function
Phosphonate ABC transporter, substrate-binding protein / Phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein / ABC transporter, phosphonate, periplasmic substrate-binding protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Binding protein component of ABC phosphonate transporter
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a binding protein component of ABC phosphonate transporter (PA3383) from Pseudomonas aeruginosa at 1.97 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 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 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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

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Assembly

Deposited unit
A: Binding protein component of ABC phosphonate transporter
B: Binding protein component of ABC phosphonate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,71233
Polymers69,7352
Non-polymers1,97731
Water11,458636
1
A: Binding protein component of ABC phosphonate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,96419
Polymers34,8671
Non-polymers1,09718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Binding protein component of ABC phosphonate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,74814
Polymers34,8671
Non-polymers88113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.890, 98.890, 170.790
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A27 - 324
2115B27 - 324

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Binding protein component of ABC phosphonate transporter /


Mass: 34867.328 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3383 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HYL8

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Non-polymers , 5 types, 667 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details(1) THE CONSTRUCT (RESIDUES 26-334) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...(1) THE CONSTRUCT (RESIDUES 26-334) 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. (2) DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS A MIXTURE OF BOTH "CCC" (PROLINE) AND "GCC" (ALANINE) AT THE POSITION CORRESPONDING TO RESIDUE 272. THE REST OF THE SEQUENCE TRACE IS CLEAN. A MIXTURE OF PROLINE AND ALANINE AT POSITION 272 IS CONSISTENT WITH THE MASS SPECTROMETRY PROFILE OF THE PURIFIED PROTEIN. HOWEVER, THE CRYSTAL APPEARS TO CONTAIN PREDOMINANTLY ALANINE AT POSITION 272 BASED ON THE ELECTRON DENSITY FIT AND CRYSTAL PACKING CONSTRAINTS. MICROHETEROGENEITY PRESENT AT POSITION 272 WAS NOT MODELED.

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.000000000M (NH4)2SO4, 0.200000000M Li2SO4, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 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
10.918371
20.979361
ReflectionResolution: 1.97→49.445 Å / Num. obs: 68965 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.138 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.37
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.97-2.050.9662.15675476461100
2.05-2.120.7252.84295057951100
2.12-2.210.5623.74786564211100
2.21-2.310.4434.74456560281100
2.31-2.430.3465.94446859611100
2.43-2.580.2917.14483160181100
2.58-2.780.2249.14595561851100
2.78-3.060.14913.14559561301100
3.06-3.50.08620.84539761321100
3.5-4.40.05131.94560362211100
4.4-49.4450.04635.2460856513199.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.97→49.445 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.02 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A UNKNOWN LIGAND (UNL), RESEMBLING GLYCEROL-3-PHOSPHATE WAS MODELED INTO THE BINDING SITE OF EACH MONOMER. THE PROTEIN IS A HOMOLOG OF PHND OF E. COLI, WHICH BINDS ALKYLPHOSPHONATE. ETHYLENE GLYCOL (EDO), SULFATE (SO4) AND CHLORIDE (CL) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3488 5.1 %RANDOM
Rwork0.158 ---
obs0.16 68909 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.02 Å2 / Biso mean: 30.65 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.24 Å20 Å2
2---0.48 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4777 0 139 636 5552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225168
X-RAY DIFFRACTIONr_bond_other_d0.0020.023606
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.976988
X-RAY DIFFRACTIONr_angle_other_deg0.93538839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73925.551245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66215922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9551523
X-RAY DIFFRACTIONr_chiral_restr0.0890.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02988
X-RAY DIFFRACTIONr_mcbond_it1.49733120
X-RAY DIFFRACTIONr_mcbond_other0.63231252
X-RAY DIFFRACTIONr_mcangle_it2.47755028
X-RAY DIFFRACTIONr_scbond_it4.5482048
X-RAY DIFFRACTIONr_scangle_it6.841111930
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1744MEDIUM POSITIONAL0.220.5
2093LOOSE POSITIONAL0.45
1744MEDIUM THERMAL1.12
2093LOOSE THERMAL1.2710
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 260 -
Rwork0.234 4743 -
all-5003 -
obs--99.84 %
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)
10.6547-0.1653-0.08520.4265-0.10740.76460.03740.023-0.0591-0.0351-0.00730.0333-0.0182-0.0341-0.03010.0230.02950.00230.0519-0.01360.05712.108934.30562.9147
23.8718-1.35191.7550.5155-0.39941.9464-0.17640.01940.43860.0170.0169-0.1473-0.33810.19420.15950.0929-0.0197-0.0010.1113-0.02640.105616.849248.161814.9432
31.64390.07270.22040.38460.22120.52870.00630.1335-0.24110.0102-0.02260.0453-0.00230.0070.01630.00220.00520.00860.1489-0.05520.1138-27.444328.506410.4203
40.5320.61920.43772.28351.46552.1043-0.04670.1650.0556-0.1055-0.11170.2309-0.1840.0210.15840.0241-0.0097-0.00960.1565-0.03820.0838-38.884446.665121.2001
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 273
2X-RAY DIFFRACTION2A274 - 331
3X-RAY DIFFRACTION3B26 - 273
4X-RAY DIFFRACTION4B274 - 327

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