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- PDB-2qml: Crystal structure of an uncharacterized protein (bh2621) from bac... -

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Basic information

Entry
Database: PDB / ID: 2qml
TitleCrystal structure of an uncharacterized protein (bh2621) from bacillus halodurans at 1.55 A resolution
ComponentsBH2621 protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


N-acyltransferase activity / siderophore biosynthetic process / response to antibiotic
Similarity search - Function
Acyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein BH2621 (NP_243487.1) from Bacillus halodurans at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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 300 BIOMOLECULE: 1,2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1,2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY INDICATES THAT THE MONOMER IS A SIGNIFICANT OLIGOMERIZATION STATE.
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: BH2621 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3596
Polymers24,0681
Non-polymers2915
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BH2621 protein
hetero molecules

A: BH2621 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71812
Polymers48,1372
Non-polymers58110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.780, 80.780, 70.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

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Components

#1: Protein BH2621 protein


Mass: 24068.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: NP_243487.1, BH2621 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9K9M4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M Sodium chloride, 2.0M Ammonium sulfate, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97920, 0.91837, 0.97891
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 20, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.918371
30.978911
ReflectionResolution: 1.55→28.56 Å / Num. obs: 34417 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.92 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 12.33
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.610.9451.33252076837199.6
1.61-1.670.5992224655983199.6
1.67-1.750.4632.6256346816199.7
1.75-1.840.3313.7236356270199.5
1.84-1.950.2145.6232126156199.6
1.95-2.10.1338.8245736482199.5
2.1-2.310.08813245266468199.6
2.31-2.650.06217.9251346606199.8
2.65-3.330.03727.4243226439199.8
3.33-28.560.02340.5244296479198.4

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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
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→28.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.676 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. ONE SODIUM ION, THREE CHLORIDE IONS AND TWO GLYCEROL MOLECULES WERE MODELED. 5. RESIDUES 1 TO 4 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. ELECTRON DENSITY NEAR RESIDUES 47, 119, 123 AND 150 IS UNMODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1733 5 %RANDOM
Rwork0.179 ---
obs0.181 34365 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 15 168 1789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221759
X-RAY DIFFRACTIONr_bond_other_d0.0020.021193
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.9412395
X-RAY DIFFRACTIONr_angle_other_deg1.07732931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6195212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7125.11686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8215314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.337154
X-RAY DIFFRACTIONr_chiral_restr0.070.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021965
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02349
X-RAY DIFFRACTIONr_nbd_refined0.210.3367
X-RAY DIFFRACTIONr_nbd_other0.1820.31263
X-RAY DIFFRACTIONr_nbtor_refined0.1820.5867
X-RAY DIFFRACTIONr_nbtor_other0.0890.5829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.5242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.341
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.539
X-RAY DIFFRACTIONr_mcbond_it1.95831113
X-RAY DIFFRACTIONr_mcbond_other0.5083402
X-RAY DIFFRACTIONr_mcangle_it2.7351689
X-RAY DIFFRACTIONr_scbond_it4.6638829
X-RAY DIFFRACTIONr_scangle_it6.18711706
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 115 -
Rwork0.28 2330 -
obs-2445 98.31 %
Refinement TLS params.Method: refined / Origin x: 62.392 Å / Origin y: 54.18 Å / Origin z: 20.684 Å
111213212223313233
T0.0199 Å2-0.0214 Å20.0097 Å2--0.0155 Å2-0.0091 Å2---0.0699 Å2
L0.6306 °20.1201 °2-0.0292 °2-0.4337 °20.2195 °2--1.1769 °2
S0.0601 Å °0.0177 Å °-0.0145 Å °0.012 Å °-0.0702 Å °0.0043 Å °0.0347 Å °-0.0864 Å °0.0102 Å °

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