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- PDB-1zel: Crystal structure of RV2827C protein from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1zel
TitleCrystal structure of RV2827C protein from Mycobacterium tuberculosis
Componentshypothetical protein Rv2827c
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RV2827C / hypothetical protein / winged-helix / helix-turn-helix / auto-rickshaw / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


replication protein C, winged helix domain / AbiEi antitoxin C-terminal domain / AbiEi antitoxin C-terminal domain / Transcriptional regulator, AbiEi antitoxin / Transcriptional regulator, AbiEi antitoxin / Phenol Hydroxylase P2 Protein / Winged helix DNA-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / AbiEi_1 domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.93 Å
AuthorsJanowski, R. / Panjikar, S. / Mueller-dieckmann, J. / Weiss, M.S. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J Struct Funct Genomics / Year: 2009
Title: Structural analysis reveals DNA binding properties of Rv2827c, a hypothetical protein from Mycobacterium tuberculosis.
Authors: Janowski, R. / Panjikar, S. / Eddine, A.N. / Kaufmann, S.H. / Weiss, M.S.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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.ptnr2_symmetry / _struct_ref_seq_dif.details / _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 Rv2827c
B: hypothetical protein Rv2827c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,20222
Polymers65,2292
Non-polymers97320
Water6,125340
1
A: hypothetical protein Rv2827c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,17012
Polymers32,6141
Non-polymers55511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Rv2827c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,03210
Polymers32,6141
Non-polymers4179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.419, 180.653, 35.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein hypothetical protein Rv2827c


Mass: 32614.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2827c / Plasmid: PETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)PLYSS / References: UniProt: Q7D6H9

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Non-polymers , 5 types, 360 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.1 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 0.1 M SODIUM ACETATE, 2 M SODIUM FORMATE, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1310.81
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9195,0.9203,0.9095
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDDec 4, 2004mirrors
MARRESEARCH2CCDFeb 19, 2005mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.811
20.91951
30.92031
40.90951
ReflectionResolution: 1.93→50 Å / Num. all: 43052 / Num. obs: 43052 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.3
Reflection shellResolution: 1.93→2 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4214 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.93→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.13 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.22455 1341 3.1 %RANDOM
Rwork0.18136 ---
all0.18269 41592 --
obs0.18269 41592 99.87 %-
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: 26.881 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---2 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.93→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 63 340 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224765
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9816525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9721.25192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13515718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1171560
X-RAY DIFFRACTIONr_chiral_restr0.0920.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023668
X-RAY DIFFRACTIONr_nbd_refined0.2170.22296
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2331
X-RAY DIFFRACTIONr_metal_ion_refined0.130.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.242
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1060.22
X-RAY DIFFRACTIONr_mcbond_it0.8211.53030
X-RAY DIFFRACTIONr_mcangle_it1.5182.54840
X-RAY DIFFRACTIONr_scbond_it3.32451852
X-RAY DIFFRACTIONr_scangle_it5.168101670
LS refinement shellResolution: 1.93→2.034 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.275 221 -
Rwork0.226 5874 -
obs-4214 99.46 %
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)
11.57250.6144-0.02781.10060.11971.46620.0558-0.05220.00530.0953-0.01360.06680.044-0.1392-0.0422-0.0438-0.01820.01420.0039-0.0049-0.03244.1731-32.116830.9006
26.63530.21410.25883.9653-0.52442.8019-0.0561-0.1727-0.00890.03950.17380.13330.0953-0.1706-0.1178-0.0755-0.0152-0.0101-0.02510.0275-0.0455.6007-19.311419.2344
30.38120.27630.04781.5017-0.37020.8085-0.04920.02370.0247-0.03610.083-0.0023-0.0596-0.0325-0.0338-0.0531-0.00910.0027-0.016-0.0027-0.014115.7963-5.09868.1177
40.8894-1.2111-0.04765.6042-2.31453.8827-0.04230.0530.02470.39530.0301-0.3079-0.33880.05130.0122-0.0228-0.0638-0.0385-0.1282-0.0151-0.06522.855212.513111.4534
53.2778-0.26340.64261.97280.64562.90170.1496-0.2903-0.27860.1562-0.02370.31520.2015-0.3835-0.1258-0.1136-0.04330.0032-0.00720.0493-0.006648.927217.718712.9161
69.8031-3.572-0.27241.79-1.30394.03810.1524-0.2156-0.3760.0140.010.16290.1379-0.1635-0.1624-0.07-0.0021-0.004-0.04990.0493-0.041750.280630.58091.3279
70.81860.1299-0.21841.1991-0.31970.6394-0.00920.0434-0.0082-0.02380.04960.0075-0.0794-0.0613-0.0404-0.0192-0.0006-0.02490.00370.0025-0.06460.408844.5569-9.8549
81.6636-0.24830.5254.1452-1.46852.4197-0.0005-0.03550.07820.1552-0.0098-0.2468-0.2677-0.05570.01030.0108-0.0031-0.0038-0.0947-0.0134-0.071667.481862.3683-7.0391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 802 - 83
2X-RAY DIFFRACTION2AA83 - 9486 - 97
3X-RAY DIFFRACTION3AA98 - 253101 - 256
4X-RAY DIFFRACTION4AA255 - 265258 - 268
5X-RAY DIFFRACTION4AA271 - 293274 - 296
6X-RAY DIFFRACTION5BB-2 - 801 - 83
7X-RAY DIFFRACTION6BB83 - 9486 - 97
8X-RAY DIFFRACTION7BB98 - 253101 - 256
9X-RAY DIFFRACTION8BB255 - 264258 - 267
10X-RAY DIFFRACTION8BB270 - 293273 - 296

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