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- PDB-3ezu: Crystal structure of multidomain protein of unknown function with... -

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Basic information

Entry
Database: PDB / ID: 3ezu
TitleCrystal structure of multidomain protein of unknown function with GGDEF-domain (NP_951600.1) from GEOBACTER SULFURREDUCENS at 1.95 A resolution
ComponentsGGDEF domain protein
KeywordsSIGNALING PROTEIN / NP_951600.1 / multidomain protein of unknown function with GGDEF-domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / GGDEF domain / unknown function
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Reverse transcriptase/Diguanylate cyclase domain ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Reverse transcriptase/Diguanylate cyclase domain / Ferritin-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Diguanylate cyclase
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of multidomain protein of unknown function with GGDEF-domain (NP_951600.1) from GEOBACTER SULFURREDUCENS at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 1.4Feb 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: GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2775
Polymers38,0911
Non-polymers1864
Water3,603200
1
A: GGDEF domain protein
hetero molecules

A: GGDEF domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,55410
Polymers76,1822
Non-polymers3728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area5830 Å2
ΔGint-36 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.550, 76.367, 64.191
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GGDEF domain protein


Mass: 38090.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: NP_951600.1, GSU0542 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q74FR4
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.2
Details: 0.2000M K2HPO4, 20.0000% PEG-3350, No Buffer pH 9.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97967,0.97953
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
30.979531
ReflectionResolution: 1.95→29.696 Å / Num. obs: 27108 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.194 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-23.70.6641.8724419780.664100
2-2.063.70.522.3712819310.52100
2.06-2.123.70.4332.9701919020.433100
2.12-2.183.70.3034681318460.303100
2.18-2.253.70.2644.6648817650.264100
2.25-2.333.70.2135.8638617320.21399.9
2.33-2.423.70.1737.1613116610.17399.8
2.42-2.523.70.158.5589215910.1599.8
2.52-2.633.70.1289.9578415570.12899.8
2.63-2.763.70.10311.8537714710.10399.8
2.76-2.913.70.09414518214000.09499.6
2.91-3.083.70.08816.3492313340.08899.3
3.08-3.33.70.07920.1451412310.07999.2
3.3-3.563.60.06923.6430011860.06998.8
3.56-3.93.70.05725.9390210620.05799
3.9-4.363.70.04827.735689660.04898.2
4.36-5.033.70.05128.131718620.05197.8
5.03-6.173.60.05126.826477360.05197.5
6.17-8.723.60.0532720365720.05396.5
8.72-29.6963.30.0622910633250.06292.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.696 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.022 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153
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 RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE FOLLOWING REGIONS HAVE POOR DENSITY: 125-133,332-336. 5. ETHYLENE GLYCOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. AN ADDITIONAL LIGAND OF UNKNOWN IDENTITY (UNL) WAS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1359 5 %RANDOM
Rwork0.184 ---
obs0.187 27087 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.34 Å2 / Biso mean: 31.028 Å2 / Biso min: 14.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å20 Å2
2--1.27 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 20 200 2784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222658
X-RAY DIFFRACTIONr_bond_other_d0.0010.021816
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9753594
X-RAY DIFFRACTIONr_angle_other_deg0.89634396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67322.975121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7971527
X-RAY DIFFRACTIONr_chiral_restr0.0810.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
X-RAY DIFFRACTIONr_mcbond_it1.82931677
X-RAY DIFFRACTIONr_mcbond_other0.5053697
X-RAY DIFFRACTIONr_mcangle_it3.00852674
X-RAY DIFFRACTIONr_scbond_it4.8528981
X-RAY DIFFRACTIONr_scangle_it7.16311914
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 105 -
Rwork0.267 1870 -
all-1975 -
obs--99.8 %
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)
10.77180.13420.09610.9010.25650.7311-0.07280.10920.0223-0.00510.04390.1383-0.0195-0.11080.02890.0078-0.0085-0.00470.05320.02290.051764.98554.4963-2.3442
23.81860.3651-0.73641.1798-0.03121.47760.0384-0.28420.2990.1046-0.02910.0373-0.1591-0.0158-0.00930.04750.02480.01140.044-0.0120.033877.657122.228123.776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 186
2X-RAY DIFFRACTION2A187 - 341

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