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- PDB-3nja: The crystal structure of the PAS domain of a GGDEF family protein... -

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Basic information

Entry
Database: PDB / ID: 3nja
TitleThe crystal structure of the PAS domain of a GGDEF family protein from Chromobacterium violaceum ATCC 12472.
ComponentsProbable GGDEF family protein
Keywordsstructural genomics / unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Complement Module; domain 1 - #100 / : / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Complement Module; domain 1 / GGDEF domain profile. ...Complement Module; domain 1 - #100 / : / PAS fold-4 / PAS fold / PAS fold-3 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Complement Module; domain 1 / GGDEF domain profile. / GGDEF domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS domain / PAS domain superfamily / Ribbon / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable GGDEF family protein
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.368 Å
AuthorsTan, K. / Wu, R. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the PAS domain of a GGDEF family protein from Chromobacterium violaceum ATCC 12472.
Authors: Tan, K. / Wu, R. / Feldmann, B. / Joachimiak, A.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Probable GGDEF family protein
B: Probable GGDEF family protein
C: Probable GGDEF family protein
D: Probable GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,01412
Polymers58,3824
Non-polymers6318
Water37821
1
A: Probable GGDEF family protein
B: Probable GGDEF family protein
hetero molecules

A: Probable GGDEF family protein
B: Probable GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,94310
Polymers58,3824
Non-polymers5616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area14490 Å2
ΔGint-76 kcal/mol
Surface area20030 Å2
MethodPISA
2
A: Probable GGDEF family protein
B: Probable GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4715
Polymers29,1912
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-39 kcal/mol
Surface area11410 Å2
MethodPISA
3
C: Probable GGDEF family protein
D: Probable GGDEF family protein
hetero molecules

C: Probable GGDEF family protein
D: Probable GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08514
Polymers58,3824
Non-polymers70210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area15200 Å2
ΔGint-82 kcal/mol
Surface area20240 Å2
MethodPISA
4
C: Probable GGDEF family protein
D: Probable GGDEF family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5427
Polymers29,1912
Non-polymers3515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-33 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.570, 65.527, 123.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-124-

CL

21D-125-

CL

DetailsExperimentally unknown. The chains A and B, C and D may form dimers respectively.

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Components

#1: Protein
Probable GGDEF family protein


Mass: 14595.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: ATCC 12472 / Gene: CV_1582 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7NXP4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris, 25% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.368→36 Å / Num. all: 20512 / Num. obs: 20512 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 27.8
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1016 / % possible all: 99

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.368→36 Å / SU ML: 0.34 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 978 5.18 %random
Rwork0.2073 ---
all0.2118 18876 --
obs0.2118 18876 91.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.964 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1323 Å20 Å2-0 Å2
2--11.9282 Å20 Å2
3----20.0604 Å2
Refinement stepCycle: LAST / Resolution: 2.368→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 36 21 3573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073676
X-RAY DIFFRACTIONf_angle_d1.0664978
X-RAY DIFFRACTIONf_dihedral_angle_d20.2291362
X-RAY DIFFRACTIONf_chiral_restr0.07510
X-RAY DIFFRACTIONf_plane_restr0.004669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3682-2.4930.36711160.30752121X-RAY DIFFRACTION77
2.493-2.64920.43221340.2732287X-RAY DIFFRACTION83
2.6492-2.85370.34861260.25742463X-RAY DIFFRACTION89
2.8537-3.14070.44431490.24712594X-RAY DIFFRACTION94
3.1407-3.59480.30281620.22172720X-RAY DIFFRACTION98
3.5948-4.52770.27211480.17592800X-RAY DIFFRACTION99
4.5277-36.08730.21561430.17072913X-RAY DIFFRACTION97
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)
10.58920.01940.41250.3641.01792.98060.23490.1409-0.0306-0.0173-0.24620.0150.0791-0.15460.00380.3702-0.0157-0.010.2669-0.02340.20557.449360.819621.8337
20.4420.05860.10010.5973-0.22772.706-0.40110.26260.0275-0.15710.2496-0.0124-0.0021-0.25140.09620.2792-0.1094-0.04180.34920.00490.212128.128141.103838.3716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B
2X-RAY DIFFRACTION2chain C or chain D

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