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- PDB-4hfs: Crystal structure of an uncharacterized protein (yncM) from Bacil... -

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Basic information

Entry
Database: PDB / ID: 4hfs
TitleCrystal structure of an uncharacterized protein (yncM) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution
ComponentsUncharacterized protein YncM
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / peptidase A4-like fold / YrpD / PF15493 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyJelly Rolls - #1270 / Protein of unknown function, YrpD / YrpD-like superfamily / Domain of unknown function, YrpD / Jelly Rolls / Sandwich / extracellular region / Mainly Beta / Uncharacterized protein YncM
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein (yncM) from Bacillus subtilis subsp. subtilis str. 168 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_radiation / software
Item: _diffrn_radiation.pdbx_diffrn_protocol / _software.classification / _software.name
Revision 1.2Feb 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 1.3Nov 6, 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: Uncharacterized protein YncM
B: Uncharacterized protein YncM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5896
Polymers46,2052
Non-polymers3844
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-64 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.000, 42.710, 119.710
Angle α, β, γ (deg.)90.000, 97.620, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21B-407-

HOH

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Components

#1: Protein Uncharacterized protein YncM


Mass: 23102.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU17690, NP_389652.1, yncM / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: O31803
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (40-250) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (40-250) 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.20M ammonium sulfate, 30.00% polyethylene glycol 4000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979122
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979122 Å / Relative weight: 1
ReflectionResolution: 1.55→38.5 Å / Num. all: 62880 / Num. obs: 62880 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.88 Å2 / Rsym value: 0.082 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.633.30.5532.23017191240.553100
1.63-1.733.30.3673.12852186250.367100
1.73-1.853.30.2224.62682680950.222100
1.85-23.30.1366.92514275970.136100
2-2.193.30.0949.32303569700.094100
2.19-2.453.30.08110.82094163350.08199.9
2.45-2.833.30.07812.11825755960.07899.8
2.83-3.473.20.06714.51497447270.06799.9
3.47-4.93.10.05616.41170337230.05699.9
4.9-38.5193.40.0616.3700620880.0699.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.55→38.52 Å / Cor.coef. Fo:Fc: 0.9487 / Cor.coef. Fo:Fc free: 0.9383 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. SO4 MOLECULES MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 3192 5.08 %RANDOM
Rwork0.1916 ---
obs0.1929 62814 99.9 %-
Displacement parametersBiso max: 92.08 Å2 / Biso mean: 25.9069 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.5509 Å20 Å20.9702 Å2
2---1.4996 Å20 Å2
3---3.0505 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 1.55→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 20 501 3641
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1627SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes521HARMONIC5
X-RAY DIFFRACTIONt_it3420HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4396SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3420HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4685HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion4.41
X-RAY DIFFRACTIONt_other_torsion2.5
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2464 240 5.18 %
Rwork0.2222 4394 -
all0.2234 4634 -
obs--99.9 %
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)
10.85310.14570.27741.10310.83092.0936-0.03170.01890.0340.10250.1569-0.09790.2220.3154-0.1252-0.05370.0365-0.0166-0.036-0.023-0.05815.171652.849916.746
21.02020.13920.50341.00920.56732.6352-0.16660.12750.006-0.04510.0853-0.0199-0.28440.28520.0813-0.0523-0.048-0.0378-0.05810.0102-0.068910.894536.005341.883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|48 - 250}A48 - 250
2X-RAY DIFFRACTION2{B|48 - 250}B48 - 250

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