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- PDB-3et6: The crystal structure of the catalytic domain of a eukaryotic gua... -

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Basic information

Entry
Database: PDB / ID: 3et6
TitleThe crystal structure of the catalytic domain of a eukaryotic guanylate cyclase
Components(Soluble guanylyl cyclase beta) x 2
KeywordsLYASE / guanylate cyclase / guanylyl cyclase / dimethylarsenic / Membrane / Transmembrane
Function / homology
Function and homology information


guanylate cyclase / guanylate cyclase activity / intracellular signal transduction / heme binding / GTP binding / cytoplasm
Similarity search - Function
Haem NO binding associated / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain ...Haem NO binding associated / Heme NO binding associated / Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / Nucleotide cyclase, GGDEF domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / NO signalling/Golgi transport ligand-binding domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Guanylate cyclase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsWinger, J.A. / Derbyshire, E.R. / Lamers, M.H. / Marletta, M.A. / Kuriyan, J.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase.
Authors: Winger, J.A. / Derbyshire, E.R. / Lamers, M.H. / Marletta, M.A. / Kuriyan, J.
History
DepositionOct 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Soluble guanylyl cyclase beta
B: Soluble guanylyl cyclase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,47410
Polymers42,7142
Non-polymers7608
Water1,78399
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-75 kcal/mol
Surface area16800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.678, 123.678, 62.822
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Soluble guanylyl cyclase beta / Guanylate cyclase


Mass: 21305.025 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: CYS at position 621 / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_187517, CYG12 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q5YLC2
#2: Protein Soluble guanylyl cyclase beta / Guanylate cyclase


Mass: 21409.008 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: CAS at position 621 / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_187517, CYG12 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3) / References: UniProt: Q5YLC2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium cacodylate, pH 5.0 - 6.4, 42-62% saturated (NH4)2HPO4, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→28.006 Å / Num. obs: 17490 / % possible obs: 96.2 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1.3 / Redundancy: 4.3 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.612
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.55-2.694.30.5211.30.521198.2
2.69-2.854.40.3242.10.324196.8
2.85-3.054.30.2053.50.205197.6
3.05-3.294.40.1225.70.122196
3.29-3.614.30.0887.10.088196.8
3.61-4.034.30.0780.07196.2
4.03-4.664.20.05211.20.052194.9
4.66-5.740.053110.053193.6
5.7-8.064.60.04613.30.046194.4
8.06-28.014.40.02722.20.027190.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AZS

1azs


Resolution: 2.55→28 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic + TLS / σ(F): 1.3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.215 1664 random
Rwork0.1716 --
obs0.1738 17490 -
all-18320 -
Displacement parametersBiso mean: 72.591 Å2
Baniso -1Baniso -2Baniso -3
1-5.0672 Å20 Å2-0 Å2
2--5.0672 Å20 Å2
3----19.5214 Å2
Refinement stepCycle: LAST / Resolution: 2.55→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 40 99 2999
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d23.839
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shellResolution: 2.55→2.625 Å
RfactorNum. reflection% reflection
Rfree0.2981 123 -
Rwork0.2607 --
obs--0.92 %
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)
1-1.17542.0971-4.39612.8281-1.31373.0945-0.2791-0.4517-0.49410.0217-0.0947-0.71170.31631.05020.14710.417-0.0628-0.07561.29710.24920.559-28.69238.4814-4.1848
21.2330.3901-0.8531.692-0.71322.49160.3551-0.70610.03520.3537-0.53660.0527-0.54720.86030.14330.4078-0.4461-0.040.94140.01530.278-41.236950.07374.92
32.0618-0.2058-3.01211.9846-1.33421.08760.0565-0.8249-0.25130.8271-0.51-0.0007-0.1191.28990.38240.4958-0.23960.00081.05520.00270.423-44.155438.345117.3622
40.7112-0.246-2.32640.8635-0.0757-0.46010.7566-0.3130.5041-0.235-0.46640.11330.05660.6087-0.30780.4387-0.3292-0.07730.52550.0570.3774-41.429255.4207-12.4317
50.37640.33290.80821.5119-0.023.698-0.10280.3698-0.02880.101-0.0876-0.26240.1571.29630.18660.07470.0006-0.03740.5570.0960.2818-41.41636.6472-16.7608
60.18130.00731.64410.61290.55412.7391-0.0023-0.0091-0.0759-0.0354-0.08140.1677-0.0223-0.02960.07140.04270.00480.01480.0926-0.01380.1859-57.750837.2414-22.3357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 467:475 or resid 578:595)A467 - 475
2X-RAY DIFFRACTION1chain A and (resid 467:475 or resid 578:595)A578 - 595
3X-RAY DIFFRACTION2chain A and (resid 476:560 or resid 569:577 or resid 596:608)A476 - 560
4X-RAY DIFFRACTION2chain A and (resid 476:560 or resid 569:577 or resid 596:608)A569 - 577
5X-RAY DIFFRACTION2chain A and (resid 476:560 or resid 569:577 or resid 596:608)A596 - 608
6X-RAY DIFFRACTION3chain A and (resid 613:651)A613 - 651
7X-RAY DIFFRACTION4chain B and (resid 467:475 or resid 578:595)B467 - 475
8X-RAY DIFFRACTION4chain B and (resid 467:475 or resid 578:595)B578 - 595
9X-RAY DIFFRACTION5chain B and (resid 476:560 or resid 569:577 or resid 596:608)B476 - 560
10X-RAY DIFFRACTION5chain B and (resid 476:560 or resid 569:577 or resid 596:608)B569 - 577
11X-RAY DIFFRACTION5chain B and (resid 476:560 or resid 569:577 or resid 596:608)B596 - 608
12X-RAY DIFFRACTION6chain B and (resid 613:651)B613 - 651

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