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- PDB-3bd0: Crystal structure of Memo, form II -

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Basic information

Entry
Database: PDB / ID: 3bd0
TitleCrystal structure of Memo, form II
ComponentsProtein MEMO1
KeywordsPEPTIDE BINDING PROTEIN / alpha/beta structure
Function / homology
Function and homology information


regulation of microtubule-based process / ERBB2 Regulates Cell Motility / nucleus / cytosol
Similarity search - Function
MEMO1 family / Memo-like protein / Protocatechuate 4,5-dioxygenase; Chain B / LigB-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein MEMO1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsQiu, C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Memo Is Homologous to Nonheme Iron Dioxygenases and Binds an ErbB2-derived Phosphopeptide in Its Vestigial Active Site.
Authors: Qiu, C. / Lienhard, S. / Hynes, N.E. / Badache, A. / Leahy, D.J.
History
DepositionNov 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Protein MEMO1
B: Protein MEMO1
C: Protein MEMO1
D: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,2445
Polymers133,1384
Non-polymers1061
Water1,13563
1
A: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3912
Polymers33,2851
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MEMO1


Theoretical massNumber of molelcules
Total (without water)33,2851
Polymers33,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein MEMO1


Theoretical massNumber of molelcules
Total (without water)33,2851
Polymers33,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein MEMO1


Theoretical massNumber of molelcules
Total (without water)33,2851
Polymers33,2851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.877, 88.307, 97.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 2 / Auth seq-ID: 5 - 297 / Label seq-ID: 1 - 293

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Protein MEMO1 / Mediator of ErbB2-driven cell motility 1 / Protein memo / C21orf19-like protein / Hepatitis C virus ...Mediator of ErbB2-driven cell motility 1 / Protein memo / C21orf19-like protein / Hepatitis C virus NS5A-transactivated protein 7 / HCV NS5A-transactivated protein 7


Mass: 33284.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEMO1, C2orf4, NS5ATP7 / Plasmid: pHT / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9Y316
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystal was grown in 22.5% PEG 3350, 0.1 M MES pH 5.5. Soaked in 5 mM ZnCl2, 22.5% PEG 3350 pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97989 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2007
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 24559 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.227 / Χ2: 0.939 / Net I/σ(I): 3.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.116.50.62624040.75899.8
3.11-3.2370.52724190.77199.9
3.23-3.387.30.42424020.83299.8
3.38-3.567.40.32824280.9599.9
3.56-3.787.40.25424231.0799.9
3.78-4.077.40.21324411.004100
4.07-4.487.40.16224581.093100
4.48-5.127.40.14124630.93100
5.12-6.447.30.16125040.863100
6.44-306.80.08426171.07599.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BCZ

3bcz


Resolution: 3.01→29.68 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.811 / SU B: 21.523 / SU ML: 0.402 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1249 5.1 %RANDOM
Rwork0.213 ---
obs0.217 24472 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.753 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2--3.57 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 3.01→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9356 0 0 70 9426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0219612
X-RAY DIFFRACTIONr_angle_refined_deg1.331.93713017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62551168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67123.509456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.221151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741556
X-RAY DIFFRACTIONr_chiral_restr0.1050.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027380
X-RAY DIFFRACTIONr_nbd_refined0.2190.24162
X-RAY DIFFRACTIONr_nbtor_refined0.3130.26484
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2530.217
X-RAY DIFFRACTIONr_mcbond_it0.6141.55991
X-RAY DIFFRACTIONr_mcangle_it0.94429400
X-RAY DIFFRACTIONr_scbond_it1.25834157
X-RAY DIFFRACTIONr_scangle_it2.1484.53617
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1172TIGHT POSITIONAL0.050.05
2B1172TIGHT POSITIONAL0.040.05
3C1172TIGHT POSITIONAL0.050.05
4D1172TIGHT POSITIONAL0.050.05
1A1167MEDIUM POSITIONAL0.540.5
2B1167MEDIUM POSITIONAL0.420.5
3C1167MEDIUM POSITIONAL0.40.5
4D1167MEDIUM POSITIONAL0.490.5
1A1172TIGHT THERMAL0.060.5
2B1172TIGHT THERMAL0.060.5
3C1172TIGHT THERMAL0.060.5
4D1172TIGHT THERMAL0.050.5
1A1167MEDIUM THERMAL0.52
2B1167MEDIUM THERMAL0.432
3C1167MEDIUM THERMAL0.442
4D1167MEDIUM THERMAL0.492
LS refinement shellResolution: 3.01→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 92 -
Rwork0.27 1650 -
all-1742 -
obs--98.03 %

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