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- PDB-2gjg: CRYSTAL STRUCTURE OF A PILZ-CONTAINING PROTEIN (PP4397) FROM PSEU... -

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Basic information

Entry
Database: PDB / ID: 2gjg
TitleCRYSTAL STRUCTURE OF A PILZ-CONTAINING PROTEIN (PP4397) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.25 A RESOLUTION
Componentshypothetical protein PP4397
KeywordsMOTOR PROTEIN / PILZ-CONTAINING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed / bacterial-type flagellum basal body / cyclic-di-GMP binding / bacterial-type flagellum-dependent cell motility
Similarity search - Function
Type III secretion system flagellar brake protein YcgR / Flagellar regulator YcgR, PilZN domain / Type III secretion system flagellar brake protein YcgR, PilZN domain / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Thrombin, subunit H ...Type III secretion system flagellar brake protein YcgR / Flagellar regulator YcgR, PilZN domain / Type III secretion system flagellar brake protein YcgR, PilZN domain / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Thrombin, subunit H / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Flagellar brake protein YcgR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_746511.1) from Pseudomonas putida KT2440 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PP4397
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9254
Polymers28,7391
Non-polymers1863
Water2,468137
1
A: hypothetical protein PP4397
hetero molecules

A: hypothetical protein PP4397
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8508
Polymers57,4772
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)89.224, 48.819, 57.476
Angle α, β, γ (deg.)90.000, 93.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein PP4397


Mass: 28738.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: NP_746511.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q88EQ6
#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.: 137 / 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: 2.11 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 277 K / pH: 5.5
Details: 35.0% 2-propanol, 5.0% PEG-1000, 0.1M Citrate pH 5.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97941, 0.97879, 0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 20, 2006
Details: Flat collimating mirror, double crystal monochromator, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.978791
30.911621
ReflectionResolution: 2.25→28.69 Å / Num. obs: 11812 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.25-2.3194.72.70.31.28470.3
2.31-2.3710030.2163.58290.216
2.37-2.4410030.1784.28270.178
2.44-2.5210030.164.87990.16
2.52-2.610030.1544.97940.154
2.6-2.6910030.1313.77470.131
2.69-2.7999.930.0947.77230.094
2.79-2.91003.10.0878.47060.087
2.9-3.0310030.06910.56720.069
3.03-3.1810030.06410.56470.064
3.18-3.3599.930.05612.25970.056
3.35-3.5699.930.04913.45990.049
3.56-3.899.42.90.05610.45320.056
3.8-4.1199.830.04214.75050.042
4.11-4.599.830.03517.34710.035
4.5-5.0399.630.03119.84340.031
5.03-5.8199.630.0415.73740.04
5.81-7.1299.430.04911.93240.049
7.12-10.0699.130.02820.62490.028
10.06-28.6993.92.80.02327.71360.023

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→28.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 17.634 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.274
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.ELECTRON DENSITY MAP SUPPORTS THE CONFIGURATION OF RESIDUE 194 WITH RAMACHANDRAN OUTLIER IN THIS MODEL. 4.ETHYLENE GLYCOL MOLECULES FROM CRYSTALIZATION CONDITION ARE BULIT IN THIS MODEL. 5.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 564 4.8 %RANDOM
Rwork0.206 ---
all0.21 ---
obs0.20976 11212 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.772 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.85 Å2
2--0.52 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.25→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 12 137 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212022
X-RAY DIFFRACTIONr_bond_other_d0.0020.021810
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9462729
X-RAY DIFFRACTIONr_angle_other_deg0.82334182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.923.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25415335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6541518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.1960.2364
X-RAY DIFFRACTIONr_nbd_other0.1750.21784
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2933
X-RAY DIFFRACTIONr_nbtor_other0.0850.21288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.216
X-RAY DIFFRACTIONr_mcbond_it0.711.51284
X-RAY DIFFRACTIONr_mcbond_other0.1291.5508
X-RAY DIFFRACTIONr_mcangle_it1.05121984
X-RAY DIFFRACTIONr_scbond_it1.583829
X-RAY DIFFRACTIONr_scangle_it2.4474.5743
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.556 38 -
Rwork0.411 775 -
obs--90.94 %
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)
12.7451-0.7583-1.08081.81940.62412.2138-0.01930.2036-0.0462-0.0149-0.03740.213-0.0025-0.17990.0567-0.13610.0316-0.0224-0.15780.0334-0.119217.883838.639615.6758
23.76010.3279-1.67852.2906-0.51622.9950.03350.27070.1262-0.05150.07390.193-0.0787-0.3162-0.1074-0.1196-0.0441-0.04-0.0893-0.0143-0.122347.114634.0825-13.1528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1302 - 131
2X-RAY DIFFRACTION2AA131 - 247132 - 248

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