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- PDB-2gpi: Crystal structure of a protein of unknown function from duf1488 f... -

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Basic information

Entry
Database: PDB / ID: 2gpi
TitleCrystal structure of a protein of unknown function from duf1488 family (shew_3726) from shewanella loihica pv-4 at 1.60 A resolution
Componentsconserved hypothetical protein
KeywordsUNKNOWN FUNCTION / Transcriptional regulation of the shikimate pathway / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyShew3726-like / Protein of unknown function DUF1488 / Shew3726-like superfamily / Protein of unknown function (DUF1488) / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta / Transcriptional regulator / :
Function and homology information
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of conserved hypothetical protein (ZP_00837230.1) from Shewanella sp. PV-4 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 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: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6752
Polymers10,6121
Non-polymers621
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.030, 83.250, 58.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein conserved hypothetical protein


Mass: 10612.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: ZP_00837230.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q33UM0, UniProt: A3QJE4*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.6
Details: 2.0M (NH4)2SO4, 0.1M Acetate, pH 4.6, 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: 0.91837, 0.97925, 0.97858
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2006 / 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
20.979251
30.978581
ReflectionResolution: 1.6→29.14 Å / Num. obs: 15507 / % possible obs: 93 % / Biso Wilson estimate: 22.412 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.660.3392.86719273787.7
1.66-1.720.2943.36380246991.2
1.72-1.80.2254.37308281192.6
1.8-1.90.1645.77655293193.5
1.9-2.020.1118.17360281394.6
2.02-2.170.08117245273695
2.17-2.390.06513.67610285094.5
2.39-2.730.05216.17428276494.4
2.730.046197751285294.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT1.701data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.472 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068
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 ...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) EDO WAS ADDED BASED ON CRYSTALLIZATION CONDITION. (4) TLS GROUPS WERE ASSIGNED WITH THE AID OF TLSMD. (4) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 778 5 %RANDOM
Rwork0.151 ---
obs0.152 15490 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--0.43 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 4 99 836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022776
X-RAY DIFFRACTIONr_bond_other_d0.0010.02498
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9241051
X-RAY DIFFRACTIONr_angle_other_deg0.95531233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.249597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42227.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11215142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.238151
X-RAY DIFFRACTIONr_chiral_restr0.0920.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02144
X-RAY DIFFRACTIONr_nbd_refined0.2240.2145
X-RAY DIFFRACTIONr_nbd_other0.1840.2490
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2388
X-RAY DIFFRACTIONr_nbtor_other0.0840.2388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2870.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.219
X-RAY DIFFRACTIONr_mcbond_it2.4993512
X-RAY DIFFRACTIONr_mcbond_other0.5233190
X-RAY DIFFRACTIONr_mcangle_it3.2135754
X-RAY DIFFRACTIONr_scbond_it5.3278329
X-RAY DIFFRACTIONr_scangle_it8.15411294
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 60 -
Rwork0.213 1075 -
obs-1135 98.52 %
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)
11.1980.2802-0.86010.8027-0.06082.86160.01-0.0363-0.1031-0.0044-0.0458-0.02630.09130.09930.0358-0.04240.00570.0035-0.02030.0129-0.0337-1.209522.148424.2315
21.24860.08020.10680.7658-0.22040.83870.00440.01690.01670.0688-0.00560.0658-0.00850.00490.0012-0.0343-0.00010.0138-0.03630.0046-0.0383-6.159428.880625.3264
31.7121-0.85470.4391.3316-0.79371.9816-0.0222-0.05590.07590.0913-0.1165-0.1846-0.04650.19950.1387-0.0374-0.0094-0.0178-0.00840.0036-0.01216.392527.720426.6934
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
110 - 241 - 25
2225 - 6526 - 66
3366 - 9067 - 91

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