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- PDB-4m1a: Crystal structure of a Domain of unknown function (DUF1904) from ... -

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Basic information

Entry
Database: PDB / ID: 4m1a
TitleCrystal structure of a Domain of unknown function (DUF1904) from Sebaldella termitidis ATCC 33386
ComponentsHypothetical protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / PROTEIN STRUCTURE INITIATIVE / DUF1904 / alpha/beta / trimeric assembly
Function / homologyProtein of unknown function DUF1904 / Domain of unknown function (DUF1904) / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta / DUF1904 domain-containing protein
Function and homology information
Biological speciesSebaldella termitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a Domain of unknown function (DUF1904) from Sebaldellatermitidis ATCC 33386
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)30,2072
Polymers30,2072
Non-polymers00
Water1,74797
1
A: Hypothetical protein

A: Hypothetical protein

A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)45,3113
Polymers45,3113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6810 Å2
ΔGint-34 kcal/mol
Surface area13950 Å2
MethodPISA
2
B: Hypothetical protein

B: Hypothetical protein

B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)45,3113
Polymers45,3113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6740 Å2
ΔGint-34 kcal/mol
Surface area14000 Å2
MethodPISA
3
A: Hypothetical protein

A: Hypothetical protein

B: Hypothetical protein

B: Hypothetical protein

A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)90,6226
Polymers90,6226
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.283, 90.283, 37.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

21A-217-

HOH

31A-226-

HOH

DetailsDimer of trimer

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Components

#1: Protein Hypothetical protein


Mass: 15103.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sebaldella termitidis (bacteria) / Strain: ATCC 33386 / Gene: Sterm_0053 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: D1AJN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate 0.1M Bis-Tris 45% 2-Methyl-2,4-pentanediol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2013 / Details: mirrors
RadiationMonochromator: Si II / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 25228 / Num. obs: 25228 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2 / Num. unique all: 1504 / % possible all: 66.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.18 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.159 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20551 1291 5.1 %RANDOM
Rwork0.17579 ---
all0.199 23937 --
obs0.17732 23937 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.11 Å2-0 Å2
2--0.11 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 97 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191844
X-RAY DIFFRACTIONr_bond_other_d0.0020.021704
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.9382494
X-RAY DIFFRACTIONr_angle_other_deg0.95233920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32623.8100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52115298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4721512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 63 -
Rwork0.164 1271 -
obs--65.94 %

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