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- PDB-1q8c: A conserved hypothetical protein from Mycoplasma genitalium shows... -

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Basic information

Entry
Database: PDB / ID: 1q8c
TitleA conserved hypothetical protein from Mycoplasma genitalium shows structural homology to NusB proteins
ComponentsHypothetical protein MG027
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NusB / hypothetical protein / MG027 / GI 3844637 / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homologyProtein of unknown function DUF1948 / Domain of unknown function (DUF1948) / N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB-like superfamily / Orthogonal Bundle / Mainly Alpha / IODIDE ION / Uncharacterized protein MG027
Function and homology information
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLiu, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2004
Title: A conserved hypothetical protein from Mycoplasma genitalium shows structural homology to nusb proteins
Authors: Liu, J. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein MG027
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,53413
Polymers17,5051
Non-polymers1,02812
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.401, 41.401, 99.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Hypothetical protein MG027


Mass: 17505.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma genitalium (bacteria) / References: UniProt: P47273
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.25 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 mg/mlprotein1drop
20.2 Msodium iodide1reservoir
320 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9790, 0.9638, 1.0086
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.96381
31.00861
ReflectionResolution: 2→25 Å / Num. all: 12019 / Num. obs: 11286 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064
Reflection shellResolution: 2→2.05 Å / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 11273 / % possible obs: 94.7 % / Num. measured all: 35519 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.8

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.457 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27153 1032 9.7 %RANDOM
Rwork0.25352 ---
obs0.25527 9565 94 %-
all-10112 --
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 mean: 40.739 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 12 61 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221102
X-RAY DIFFRACTIONr_bond_other_d0.0020.021033
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.971482
X-RAY DIFFRACTIONr_angle_other_deg0.94132419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7655130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.16715227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02203
X-RAY DIFFRACTIONr_nbd_refined0.250.2311
X-RAY DIFFRACTIONr_nbd_other0.2390.21151
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.2606
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2230.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.390.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3710.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.2431.5660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41221068
X-RAY DIFFRACTIONr_scbond_it0.8113442
X-RAY DIFFRACTIONr_scangle_it1.3034.5414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.369 64
Rwork0.356 534
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)
14.1881-0.25950.78483.77320.21966.1682-0.2453-0.18710.28610.04620.05140.513-0.1416-0.56410.19390.01170.0227-0.01650.0977-0.07010.113328.9313.607781.6041
26.07531.9945-0.37524.67510.32455.3716-0.20930.19380.5389-0.17940.07330.9987-0.1228-0.85330.1360.09340.079-0.11080.2256-0.04910.316822.80557.444674.2219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 8812 - 88
2X-RAY DIFFRACTION2AA97 - 15197 - 151
Software
*PLUS
Version: 5.1.19 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 24.99 Å / % reflection Rfree: 8 % / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.47

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