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- PDB-3vol: X-ray Crystal Structure of PAS-HAMP Aer2 in the CN-bound Form -

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Basic information

Entry
Database: PDB / ID: 3vol
TitleX-ray Crystal Structure of PAS-HAMP Aer2 in the CN-bound Form
ComponentsAerotaxis transducer Aer2
KeywordsSIGNALING PROTEIN / heme / oxygen sensor protein / PAS / HAMP / cyanomet / CN-bound
Function / homology
Function and homology information


positive aerotaxis / aerotaxis / chemotaxis / transmembrane signaling receptor activity / signal transduction / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
HAMP N-terminal domain 3 / : / : / HAMP N-terminal domain 3 / Methyl-accepting chemotaxis protein McpB, second HAMP domain / Methyl-accepting chemotaxis protein McpB, first HAMP domain / HAMP domain / PAS domain / : / Chemotaxis methyl-accepting receptor ...HAMP N-terminal domain 3 / : / : / HAMP N-terminal domain 3 / Methyl-accepting chemotaxis protein McpB, second HAMP domain / Methyl-accepting chemotaxis protein McpB, first HAMP domain / HAMP domain / PAS domain / : / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain profile. / HAMP domain / PAS domain / Beta-Lactamase / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Methyl-accepting chemotaxis protein McpB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.399 Å
AuthorsSawai, H. / Sugimoto, H. / Shiro, Y. / Aono, S.
CitationJournal: Chem.Commun.(Camb.) / Year: 2012
Title: Structural basis for oxygen sensing and signal transduction of the heme-based sensor protein Aer2 from Pseudomonas aeruginosa
Authors: Sawai, H. / Sugimoto, H. / Shiro, Y. / Ishikawa, H. / Mizutani, Y. / Aono, S.
History
DepositionJan 27, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Aerotaxis transducer Aer2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4423
Polymers25,8001
Non-polymers6432
Water19811
1
A: Aerotaxis transducer Aer2
hetero molecules

A: Aerotaxis transducer Aer2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8856
Polymers51,6002
Non-polymers1,2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area2770 Å2
ΔGint-12 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.020, 83.020, 107.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Aerotaxis transducer Aer2


Mass: 25799.926 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 173-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO-1 / Gene: aer2, PA0176 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I6V6
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6M ammonium sulfate, 0.1M Trizma/HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 23, 2011
Diffraction measurementDetails: 1.00 degrees, 2.6 sec, detector distance 200.00 mm / Method: \w scans
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.048 / Number: 196341
ReflectionResolution: 2.399→50 Å / Num. obs: 9116 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 66.58
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 22 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 5.723 / Rsym value: 0.569 / % possible all: 100
Cell measurementReflection used: 196341

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.79 Å43.12 Å
Translation2.79 Å43.12 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 9083
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.65-100390.841503
5.18-6.6544.50.851502
4.49-5.1833.10.891501
4.06-4.4928.40.881510
3.75-4.0632.50.859503
3.52-3.7535.70.836512
3.33-3.5236.60.828504
3.18-3.3345.10.741512
3.05-3.1845.50.705507
2.94-3.0549.10.635504
2.84-2.9462.30.478504
2.76-2.8470.90.407515
2.68-2.7680.80.282501
2.61-2.6887.90.106503
2.55-2.6189.60.145506
2.5-2.5595.4507
2.4-2.589.10.192989

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DM6.1phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
HKL-2000data reduction
RefinementResolution: 2.399→29.904 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.751 / SU ML: 0.42 / σ(F): 0 / Phase error: 29.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 433 4.77 %
Rwork0.2233 8640 -
obs0.2253 9073 99.96 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.182 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 137.04 Å2 / Biso mean: 64.8455 Å2 / Biso min: 29.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.9285 Å2-0 Å2-0 Å2
2--0.9285 Å20 Å2
3----1.8571 Å2
Refinement stepCycle: LAST / Resolution: 2.399→29.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 45 11 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021135
X-RAY DIFFRACTIONf_angle_d2.0081543
X-RAY DIFFRACTIONf_dihedral_angle_d18.482409
X-RAY DIFFRACTIONf_chiral_restr0.119163
X-RAY DIFFRACTIONf_plane_restr0.007206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3995-2.74650.39141570.34812776
2.7465-3.45950.28571260.24552857
3.4595-29.90610.23911500.19663007
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)
10.7130.2072-0.15180.2458-0.04370.1567-0.00660.1451-0.406-0.00930.0411-0.2654-0.0270.1263-0.0030.4173-0.1438-0.05360.6987-0.02240.73536.380812.265562.086
20.62870.4570.05570.6211-0.29180.713-0.92930.004-0.1977-1.18560.01551.0532-0.3580.11680.1770.6174-0.0759-0.57340.2754-0.13290.469811.824522.878451.8577
30.0263-0.0664-0.06280.3909-0.19940.39350.03030.1297-0.0248-0.7095-0.07620.3096-0.13950.17120.00330.9158-0.3513-0.5085-0.0294-0.4706-0.255419.846820.909345.0215
41.34830.6146-0.12320.90180.66940.80160.0615-0.1642-0.2333-0.3218-0.1485-0.066-0.04080.05430.04090.3252-0.0263-0.15110.27080.0460.369621.768321.649559.6333
50.3941-0.3575-0.11230.40680.3040.65870.31970.15320.1347-0.1440.1396-0.36490.2690.1242-0.27280.5454-0.0222-0.05640.377-0.02920.517326.578648.099356.6254
60.0017-0.0066-0.00080.00020.00250.00130.0046-0.0946-0.00160.00710.0254-0.0227-0.08770.072-00.3547-0.0243-0.00750.447-0.03350.38623.431623.712753.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 169:179)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 180:215)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 216:236)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 237:286)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 287:306)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 401:401)

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