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- PDB-3e98: CRYSTAL STRUCTURE OF a GAF domain containing protein that belongs... -

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Basic information

Entry
Database: PDB / ID: 3.0E+98
TitleCRYSTAL STRUCTURE OF a GAF domain containing protein that belongs to Pfam DUF484 family (PA5279) FROM PSEUDOMONAS AERUGINOSA AT 2.43 A RESOLUTION
ComponentsGAF Domain of Unknown Function
KeywordsUNKNOWN FUNCTION / GAF DOMAIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyProtein of unknown function DUF484 / Protein of unknown function, DUF484 / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / DUF484 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a GAF Domain with Unknown Function (NP_253966.1) from PSEUDOMONAS AERUGINOSA at 2.43 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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
Revision 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAF Domain of Unknown Function
B: GAF Domain of Unknown Function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7875
Polymers56,6012
Non-polymers1863
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-17 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.841, 88.114, 60.963
Angle α, β, γ (deg.)90.000, 107.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GAF Domain of Unknown Function


Mass: 28300.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: NP_253966.1, orf2332, PA5279 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q51565
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2000M Ca(OAc)2, 10.0000% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97975
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / 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
20.979751
ReflectionResolution: 2.43→29.412 Å / Num. obs: 20453 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 59.268 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.038
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.689 / % possible all: 99.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.43→29.412 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 15.957 / SU ML: 0.18 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.253
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. NCS RESTRAINTS WERE NOT APPLIED DUE TO LARGE DIFFERENCES BETWEEN THE TWO CHAINS. 5. EDO MODELED ARE PRESENT IN CRYO CONDITION. 6. ELECTRON DENSITY FOR THE HIS-TAGS AND ~50 N-TERMINAL RESIDUES WAS NOT OBSERVED. AS A RESULT, THE HIS-TAGS (RESIDUES -18 TO 0 FROM BOTH CHAINS) AND RESIDUES A1-47 AND B1-45 ARE LIKELY DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1044 5.1 %RANDOM
Rwork0.211 ---
obs0.214 20436 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.97 Å2 / Biso mean: 53.003 Å2 / Biso min: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0.36 Å2
2---1.13 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.43→29.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2687 0 12 75 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212757
X-RAY DIFFRACTIONr_bond_other_d0.0010.021871
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9753728
X-RAY DIFFRACTIONr_angle_other_deg0.85234531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8885354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.50322.479121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42415463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5371528
X-RAY DIFFRACTIONr_chiral_restr0.0650.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
X-RAY DIFFRACTIONr_nbd_refined0.2020.2552
X-RAY DIFFRACTIONr_nbd_other0.1770.21920
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21360
X-RAY DIFFRACTIONr_nbtor_other0.0860.21511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3380.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.28
X-RAY DIFFRACTIONr_mcbond_it1.59531794
X-RAY DIFFRACTIONr_mcbond_other0.2663719
X-RAY DIFFRACTIONr_mcangle_it2.79452805
X-RAY DIFFRACTIONr_scbond_it4.54881042
X-RAY DIFFRACTIONr_scangle_it6.48911920
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 75 -
Rwork0.296 1427 -
all-1502 -
obs--99.67 %
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)
10.429-0.09170.33041.92390.15510.5579-0.06020.11350.0221-0.07880.08090.0219-0.0970.0435-0.0207-0.12290.00490.0065-0.0148-0.0077-0.067530.250619.174650.4087
20.2584-0.24580.02471.31960.05120.5683-0.0969-0.2253-0.09120.26920.13560.0257-0.0713-0.0584-0.0388-0.07670.00880.00380.04170.0165-0.020111.478217.922470.7463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA48 - 22567 - 244
2X-RAY DIFFRACTION2BB46 - 22565 - 244

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