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- PDB-3bcz: Crystal structure of Memo -

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Basic information

Entry
Database: PDB / ID: 3bcz
TitleCrystal structure of Memo
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_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_conn.pdbx_leaving_atom_flag / _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)135,0999
Polymers134,6394
Non-polymers4605
Water8,341463
1
A: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8443
Polymers33,6601
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7522
Polymers33,6601
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7522
Polymers33,6601
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein MEMO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7522
Polymers33,6601
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.826, 88.849, 98.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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

Dom-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
15AA5 - 2971 - 293
25BB5 - 2971 - 293
36CC6 - 2972 - 293
45DD5 - 2971 - 293

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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: 33659.734 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22.5% PEG 3350, 0.1 M MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 71140 / % possible obs: 99 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.186.50.606198.2
2.18-2.266.60.477198.4
2.26-2.376.60.366198.6
2.37-2.496.70.32198.8
2.49-2.656.60.251198.9
2.65-2.856.60.195199.1
2.85-3.146.60.139199.3
3.14-3.596.60.095199.3
3.59-4.526.50.072199.6
4.52-306.30.072199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.755 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 3598 5.1 %RANDOM
Rwork0.18298 ---
obs0.18537 71115 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.812 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20 Å2
2--2.86 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9353 0 30 463 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0219647
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9413065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3451175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6623.479457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.704151605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.051557
X-RAY DIFFRACTIONr_chiral_restr0.1420.21378
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.24197
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.26446
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2507
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.56065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35329419
X-RAY DIFFRACTIONr_scbond_it2.60634207
X-RAY DIFFRACTIONr_scangle_it3.7484.53642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1164medium positional0.160.5
2B1164medium positional0.140.5
3C1164medium positional0.240.5
4D1164medium positional0.180.5
1A1152loose positional0.535
2B1152loose positional0.585
3C1152loose positional0.645
4D1152loose positional0.545
1A1164medium thermal0.862
2B1164medium thermal12
3C1164medium thermal1.242
4D1164medium thermal1.032
1A1152loose thermal1.9110
2B1152loose thermal2.0110
3C1152loose thermal2.1810
4D1152loose thermal2.1310
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 281 -
Rwork0.216 4780 -
obs--97.12 %
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)
11.72680.1438-0.31941.9436-0.49422.0931-0.0527-0.0405-0.15590.0101-0.0252-0.03950.13560.01740.07790.0525-0.0053-0.0166-0.04250.03320.0414-17.3272-28.728917.3472
21.0795-0.0481-0.16350.8163-0.35941.983-0.0410.01890.03610.0818-0.0304-0.0752-0.06770.02860.07140.0268-0.009-0.0118-0.03380.03290.0666-16.1036-20.69429.4553
32.29090.18010.23151.1679-0.11941.712-0.0582-0.13280.0571-0.00870.0303-0.0588-0.09240.13670.02790.0347-0.00780.00780.03110.0172-0.008920.7012-11.5635-4.4569
41.1932-0.1532-0.0540.6272-0.00331.5831-0.0498-0.0291-0.1482-0.03750.02870.01490.05220.05110.02110.019-0.02820.01160.02430.02090.031617.3789-19.12-12.2393
53.06760.12310.09621.23230.22231.511-0.03370.40710.3169-0.01120.00840.0865-0.17370.00770.02530.0571-0.01280.02020.15770.08170.0479-19.1492-12.3336-44.7606
61.61440.0553-0.18250.73510.33611.2603-0.02960.2492-0.0345-0.0311-0.0179-0.05920.02360.13640.04750.0322-0.00860.01230.09010.03530.0407-15.8389-19.7262-36.7421
72.0877-0.2802-0.34311.62220.05521.8240.01050.0192-0.16910.027-0.0079-0.00780.1862-0.0283-0.00260.0571-0.0236-0.0277-0.0225-0.02050.023619.3313-29.568831.9728
80.9590.0734-0.41420.6379-0.07042.04820.0242-0.08630.0207-0.00880.01390.0281-0.0546-0.0713-0.03810.02910.0008-0.0014-0.0017-0.00630.035617.5283-21.312139.5684
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 871 - 83
2X-RAY DIFFRACTION2AA88 - 29784 - 293
3X-RAY DIFFRACTION3BB5 - 871 - 83
4X-RAY DIFFRACTION4BB88 - 29784 - 293
5X-RAY DIFFRACTION5CC6 - 872 - 83
6X-RAY DIFFRACTION6CC88 - 29784 - 293
7X-RAY DIFFRACTION7DD5 - 871 - 83
8X-RAY DIFFRACTION8DD88 - 29784 - 293

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