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- PDB-1ml8: structural genomics -

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Basic information

Entry
Database: PDB / ID: 1ml8
Titlestructural genomics
Componentshypothetical protein (crp region)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / N-terminal domain of TfIIb - #10 / K homology (KH) domain / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich ...OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / N-terminal domain of TfIIb - #10 / K homology (KH) domain / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein YhfA / Protein YhfA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsKorolev, S. / Skarina, T. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structural genomics
Authors: Korolev, S. / Skarina, T. / Joachimiak, A. / Edwards, A. / Savchenko, A.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein (crp region)


Theoretical massNumber of molelcules
Total (without water)14,5251
Polymers14,5251
Non-polymers00
Water00
1
A: hypothetical protein (crp region)

A: hypothetical protein (crp region)


Theoretical massNumber of molelcules
Total (without water)29,0492
Polymers29,0492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+4/31
Unit cell
Length a, b, c (Å)76.352, 76.352, 107.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein hypothetical protein (crp region)


Mass: 14524.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P24246, UniProt: P0ADX1*PLUS
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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG4K;0.2M Ammon. Sulph., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945; 0.97934
DetectorType: SBC-2 / Detector: CCD / Date: Apr 21, 2002
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979341
ReflectionResolution: 2.6→50 Å / Num. obs: 10742 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 27
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.8 / % possible all: 95.8

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.05refinement
d*TREKdata reduction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 280 4.6 %RANDOM
Rwork0.22798 ---
obs0.22976 5798 99.1 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.957 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å21.18 Å20 Å2
2--2.37 Å20 Å2
3----3.55 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms964 0 0 0 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021976
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9531321
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07915165
X-RAY DIFFRACTIONr_chiral_restr0.1190.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.2372
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2751.5646
X-RAY DIFFRACTIONr_mcangle_it2.39721026
X-RAY DIFFRACTIONr_scbond_it3.8793330
X-RAY DIFFRACTIONr_scangle_it6.4754.5295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 29
Rwork0.246 393
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)
14.4794-0.3380.03551.4345-1.59174.7624-0.1430.0664-0.22870.28630.12160.06530.160.00390.02140.07810.08550.00290.09490.01710.16315.669628.448680.0292
22.1528-0.27941.48292.1114-0.61765.29450.1930.2833-0.3206-0.12080.0050.04250.55460.0439-0.1980.05780.0325-0.03590.2608-0.02740.18518.792118.763257.6584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 351 - 35
2X-RAY DIFFRACTION2AA36 - 13436 - 134

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