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- PDB-3bfm: Crystal structure of a biotin protein ligase-like protein of unkn... -

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Basic information

Entry
Database: PDB / ID: 3bfm
TitleCrystal structure of a biotin protein ligase-like protein of unknown function (tm1040_0394) from silicibacter sp. tm1040 at 1.70 A resolution
ComponentsBiotin protein ligase-like protein of unknown function
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


protein modification process => GO:0036211 / metal ion binding
Similarity search - Function
Domain of unknown function DUF4444 / Domain of unknown function (DUF4444) / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / SH3 type barrels. / Roll / 2-Layer Sandwich ...Domain of unknown function DUF4444 / Domain of unknown function (DUF4444) / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / SH3 type barrels. - #100 / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / SH3 type barrels. / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesSilicibacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of biotin protein ligase-like protein of unknown function (YP_612389.1) from Silicibacter sp. TM1040 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE 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: Biotin protein ligase-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8814
Polymers25,3871
Non-polymers4953
Water3,045169
1
A: Biotin protein ligase-like protein of unknown function
hetero molecules

A: Biotin protein ligase-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7638
Polymers50,7732
Non-polymers9896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.760, 36.560, 71.000
Angle α, β, γ (deg.)90.000, 99.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-236-

CA

21A-239-

HOH

31A-250-

HOH

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Components

#1: Protein Biotin protein ligase-like protein of unknown function /


Mass: 25386.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter sp. (bacteria) / Strain: TM1040 / Gene: YP_612389.1, TM1040_0394 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GJN9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 0.2M Ca(OAc)2, 40.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97953, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979531
30.979391
ReflectionResolution: 1.7→29.553 Å / Num. obs: 24223 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.33 % / Biso Wilson estimate: 21.03 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.08
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.80.5321.6117737112195.1
1.8-1.90.4472.3102415818197.2
1.9-20.3283.582934702197.4
2-2.070.2584.549882805197.9
2.07-2.150.1995.649572788197.8
2.15-2.250.1666.451482929198.6
2.25-2.370.1357.251012887198.2
2.37-2.520.1048.550802866198.6
2.52-2.710.0799.749662816198.5
2.71-2.990.06311.450872972198.5
2.99-3.420.05113.749072824198.5
3.42-4.30.04615.850472859198.5
4.3-29.5530.0371751522861197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.553 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.515 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.114
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. THE LOOP BETWEEN RESIDUES 134-138 HAS POOR DENSITY. 4. CALCIUM IONS AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1211 5 %RANDOM
Rwork0.179 ---
obs0.182 24219 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.71 Å2
2---0.44 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 14 169 1887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221803
X-RAY DIFFRACTIONr_bond_other_d0.0010.021189
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9782477
X-RAY DIFFRACTIONr_angle_other_deg0.93132912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89823.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.231513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022045
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
X-RAY DIFFRACTIONr_nbd_refined0.2160.2344
X-RAY DIFFRACTIONr_nbd_other0.2030.21261
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2869
X-RAY DIFFRACTIONr_nbtor_other0.0880.2970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2120
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0060.21
X-RAY DIFFRACTIONr_mcbond_it2.1431200
X-RAY DIFFRACTIONr_mcbond_other0.563477
X-RAY DIFFRACTIONr_mcangle_it3.23751865
X-RAY DIFFRACTIONr_scbond_it5.1488701
X-RAY DIFFRACTIONr_scangle_it7.54811604
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 101 -
Rwork0.288 1659 -
all-1760 -
obs--96.17 %

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