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- PDB-2amh: Crystal Structure of Maf-like Protein Tbru21784AAA from T.brucei -

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Basic information

Entry
Database: PDB / ID: 2amh
TitleCrystal Structure of Maf-like Protein Tbru21784AAA from T.brucei
Componentsseptum formation protein MAF homologue, putative
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 2 domain alpha-beta motif / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyMaf protein - #10 / Maf protein / Alpha-Beta Complex / Alpha Beta / : / :
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsCaruthers, J. / Merritt, E. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Crystal Structure of Maf-like Protein Tbru21784AAA from T.brucei
Authors: Caruthers, J. / Merritt, E. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionAug 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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_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_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.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.value / _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_conn.ptnr2_label_seq_id / _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: septum formation protein MAF homologue, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9956
Polymers22,6381
Non-polymers3575
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.068, 97.068, 48.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein septum formation protein MAF homologue, putative


Mass: 22637.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pET 14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 pLysS / References: GenBank: 70834870
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 20K, MnSO4, NaoAc, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9791
SYNCHROTRONSSRL BL1-520.9794, 0.9796, 0.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 3, 2005
ADSC QUANTUM 42CCDMay 15, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1ALS monochromatorSINGLE WAVELENGTHMx-ray1
2SSRL monochromaterMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.97961
40.95371
Reflection

Av σ(I) over netI: 21.9 / Number: 6062 / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / D res high: 2.7 Å / D res low: 68.26 Å / % possible obs: 97.2 / Redundancy: 3.3 %

ID
1
2
3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.5426.8296.910.0230.0233.3
6.048.5410010.020.023.4
4.936.0410010.020.023.6
4.274.9310010.020.023.6
3.824.2710010.0240.0243.6
3.493.8210010.030.033.6
3.233.4910010.0410.0413.6
3.023.2310010.0620.0623.6
2.853.0297.510.070.072.9
2.72.858410.0840.0842.4
8.5426.8296.920.0230.0233.3
6.048.5410020.020.023.4
4.936.0410020.020.023.6
4.274.9310020.020.023.6
3.824.2710020.0240.0243.6
3.493.8210020.030.033.6
3.233.4910020.0410.0413.6
3.023.2310020.0620.0623.6
2.853.0297.520.070.072.9
2.72.858420.0840.0842.4
8.5426.8296.930.0230.0233.3
6.048.5410030.020.023.4
4.936.0410030.020.023.6
4.274.9310030.020.023.6
3.824.2710030.0240.0243.6
3.493.8210030.030.033.6
3.233.4910030.0410.0413.6
3.023.2310030.0620.0623.6
2.853.0297.530.070.072.9
2.72.858430.0840.0842.4
ReflectionResolution: 2→18 Å / Num. obs: 15517 / % possible obs: 99.8 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 6.5
Reflection shellResolution: 2→2.11 Å / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 2251 / Rsym value: 0.224 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97913.39-8.4
13 wavelength20.97884.74-6.49
13 wavelength30.95373.53-3.4
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se39.9810.3520.030.0031.107
2Se31.9830.2310.1780.2640.87
3Se35.230.0920.1840.2881.003
4Se36.8080.0450.2420.060.961
5Se38.680.1910.1890.40.855
Phasing dmFOM : 0.82 / FOM acentric: 0.83 / FOM centric: 0.77 / Reflection: 6152 / Reflection acentric: 5700 / Reflection centric: 452
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-24.280.940.950.928022555
4.8-7.70.940.960.8584074298
3.9-4.80.950.950.89106197487
3.4-3.90.910.910.86105898375
2.9-3.40.780.80.5818741759115
2.7-2.90.540.540.351039101722

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
Blu-Icedata collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→18 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.618 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 771 5 %RANDOM
Rwork0.197 ---
all0.199 ---
obs0.199 15471 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.606 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 13 86 1613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221546
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9672087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2195193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38723.05672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66315269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.751516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021158
X-RAY DIFFRACTIONr_nbd_refined0.1820.2641
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.25
X-RAY DIFFRACTIONr_mcbond_it0.6951.51009
X-RAY DIFFRACTIONr_mcangle_it1.10921560
X-RAY DIFFRACTIONr_scbond_it1.8623601
X-RAY DIFFRACTIONr_scangle_it2.944.5527
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 67 -
Rwork0.199 1075 -
all-1142 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 20.465 Å / Origin y: 11.927 Å / Origin z: 6.403 Å
111213212223313233
T-0.0293 Å2-0.0216 Å20.0176 Å2--0.0442 Å2-0.0097 Å2---0.046 Å2
L1.2026 °2-0.5243 °2-0.5897 °2-1.7806 °21.3753 °2--1.8852 °2
S-0.0838 Å °0.1261 Å °-0.1664 Å °0.2151 Å °-0.062 Å °0.067 Å °0.2255 Å °0.0516 Å °0.1458 Å °
Refinement TLS groupSelection: ALL

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