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- PDB-4jm1: Crystal structure of a protein with alpha-lytic protease prodomai... -

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Basic information

Entry
Database: PDB / ID: 4jm1
TitleCrystal structure of a protein with alpha-lytic protease prodomain-like fold (BDI_0842) from Parabacteroides distasonis ATCC 8503 at 1.40 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / ORFan / new alpha/beta fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyGMP Synthetase; Chain A, domain 3 - #300 / : / Hypothetical protein BDI_0842 / GMP Synthetase; Chain A, domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta / BDI-0842-like domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BDI_0842) from Parabacteroides distasonis ATCC 8503 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 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 1.5Nov 27, 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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0733
Polymers8,9491
Non-polymers1242
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.405, 45.673, 48.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 8948.997 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_0842, YP_001302234.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LA98
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-108 OF 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8.0% ethylene glycol, 20.0% polyethylene glycol 10000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97917,0.88557,0.97849
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.885571
30.978491
ReflectionResolution: 1.4→29.529 Å / Num. obs: 16677 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.784 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.4-1.450.5131.96396306697.7
1.45-1.510.3422.96653316797.7
1.51-1.580.2663.66184307797.3
1.58-1.660.18456351298398.7
1.66-1.760.146.56289295298.2
1.76-1.90.0958.96453316797.3
1.9-2.090.05614.66639305597.8
2.09-2.390.03919.46273299496.2
2.39-3.010.03124.46763307797.7
3.010.02132.36436300594.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.529 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.853 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.055
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. 6. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1679 845 5.1 %RANDOM
Rwork0.1289 ---
obs0.1309 16642 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 55.44 Å2 / Biso mean: 18.916 Å2 / Biso min: 9.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms622 0 8 148 778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022688
X-RAY DIFFRACTIONr_bond_other_d0.0010.02475
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.981928
X-RAY DIFFRACTIONr_angle_other_deg0.9231182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.056597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91926.89729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30215133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.339151
X-RAY DIFFRACTIONr_chiral_restr0.0840.2104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02127
X-RAY DIFFRACTIONr_mcbond_it2.3593437
X-RAY DIFFRACTIONr_mcbond_other1.2223186
X-RAY DIFFRACTIONr_mcangle_it3.5125700
X-RAY DIFFRACTIONr_scbond_it4.5918251
X-RAY DIFFRACTIONr_scangle_it6.72811221
X-RAY DIFFRACTIONr_rigid_bond_restr1.76131163
X-RAY DIFFRACTIONr_sphericity_free6.4973151
X-RAY DIFFRACTIONr_sphericity_bonded3.20231151
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 66 -
Rwork0.188 1159 -
all-1225 -
obs--99.19 %

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