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- PDB-3m6j: Crystal structure of unknown function protein from Leptospirillum... -

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Basic information

Entry
Database: PDB / ID: 3m6j
TitleCrystal structure of unknown function protein from Leptospirillum rubarum
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyFerritin - #40 / Ferritin / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein from Leptospirillum rubarum
Authors: Chang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Dec 1, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_conn / struct_ref / struct_ref_seq / 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 / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _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: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6256
Polymers66,5544
Non-polymers712
Water9,332518
1
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3133
Polymers33,2772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-21 kcal/mol
Surface area14090 Å2
MethodPISA
2
C: uncharacterized protein
D: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3133
Polymers33,2772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-24 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.843, 58.275, 93.279
Angle α, β, γ (deg.)90.00, 100.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
uncharacterized protein


Mass: 16638.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Gene: UBAL2_80490123 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2009
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 43406 / Num. obs: 43384 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 42.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 6.68 / Num. unique all: 2149 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.731 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21658 2188 5.1 %RANDOM
Rwork0.17702 ---
all0.17907 43299 --
obs0.17907 43299 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-1.03 Å2
2--0.27 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 2 518 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9685883
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1825530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34222.311212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85115768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8851557
X-RAY DIFFRACTIONr_chiral_restr0.0940.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213283
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9021.52646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77224280
X-RAY DIFFRACTIONr_scbond_it2.92931697
X-RAY DIFFRACTIONr_scangle_it5.14.51603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.896→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 170 -
Rwork0.198 2880 -
obs-3050 99.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20170.0493-0.25260.65850.49482.3909-0.0026-0.00910.0049-0.0524-0.02280.03430.0385-0.160.02540.02590.0053-0.00160.0317-0.00660.053324.6003-0.58840.8198
20.4348-0.06280.66160.6217-0.33813.3612-0.0368-0.02880.004-0.0433-0.0119-0.0347-0.04380.21740.04860.009-0.0016-0.00470.04210.0140.049549.0023-2.2229-0.1053
32.42520.36430.13391.1249-0.01491.4726-0.0049-0.08870.05480.10320.06510.0371-0.03810.012-0.06030.06860.004-0.00160.00960.00020.007624.639413.894657.8642
42.1593-0.0822-0.12121.1783-0.23051.45890.00980.0514-0.0617-0.00720.04620.00660.03190.0053-0.0560.0415-0.0062-0.01850.00560.0030.015923.014111.819632.2255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 141
2X-RAY DIFFRACTION2B5 - 140
3X-RAY DIFFRACTION3C5 - 139
4X-RAY DIFFRACTION4D5 - 142

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