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- PDB-2dg2: Crystal Structure of Mouse Apolipoprotein A-I Binding Protein -

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Basic information

Entry
Database: PDB / ID: 2dg2
TitleCrystal Structure of Mouse Apolipoprotein A-I Binding Protein
ComponentsApolipoprotein A-I binding protein
KeywordsPROTEIN BINDING / Disordered N-terminus
Function / homology
Function and homology information


membrane raft distribution / NAD(P)H-hydrate epimerase / NAD(P)HX epimerase activity / metabolite repair / nicotinamide nucleotide metabolic process / regulation of cholesterol efflux / : / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis ...membrane raft distribution / NAD(P)H-hydrate epimerase / NAD(P)HX epimerase activity / metabolite repair / nicotinamide nucleotide metabolic process / regulation of cholesterol efflux / : / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis / cell body / cilium / nucleotide binding / mitochondrion / extracellular space / metal ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
YjeF N-terminal domain-containing protein NAXE-like / YjeF N-terminal domain / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsShumilin, I.A. / Jha, K.N. / Zheng, H. / Chruszcz, M. / Cymborowski, M. / Herr, J.C. / Minor, W.
CitationJournal: Endocrinology / Year: 2008
Title: Biochemical and structural characterization of apolipoprotein A-I binding protein, a novel phosphoprotein with a potential role in sperm capacitation.
Authors: Jha, K.N. / Shumilin, I.A. / Digilio, L.C. / Chertihin, O. / Zheng, H. / Schmitz, G. / Visconti, P.E. / Flickinger, C.J. / Minor, W. / Herr, J.C.
History
DepositionMar 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apolipoprotein A-I binding protein
B: Apolipoprotein A-I binding protein
C: Apolipoprotein A-I binding protein
D: Apolipoprotein A-I binding protein
E: Apolipoprotein A-I binding protein
F: Apolipoprotein A-I binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,74618
Polymers178,9566
Non-polymers78912
Water3,801211
1
A: Apolipoprotein A-I binding protein
B: Apolipoprotein A-I binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9156
Polymers59,6522
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Apolipoprotein A-I binding protein
D: Apolipoprotein A-I binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9156
Polymers59,6522
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-73 kcal/mol
Surface area18760 Å2
MethodPISA
3
E: Apolipoprotein A-I binding protein
F: Apolipoprotein A-I binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9156
Polymers59,6522
Non-polymers2634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-73 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.855, 125.745, 163.620
Angle α, β, γ (deg.)90.00, 106.56, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 27 - 258 / Label seq-ID: 28 - 259

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
51EE
61FF
12AA
22BB
32CC
42DD
52EE
62FF

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a dimer, three of which are present in the asymmetric unit

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Components

#1: Protein
Apolipoprotein A-I binding protein


Mass: 29826.068 Da / Num. of mol.: 6 / Fragment: residues 0-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apoa1bp / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 37231544, UniProt: Q8K4Z3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.5M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97898 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 15, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.45→80 Å / Num. all: 69794 / Num. obs: 69794 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.4 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→80 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 16.524 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22844 3691 5 %RANDOM
Rwork0.20612 ---
obs0.20724 69734 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.881 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å22.7 Å2
2---1.93 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10830 0 36 211 11077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02211160
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210044
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.99715204
X-RAY DIFFRACTIONr_angle_other_deg0.952323586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57251392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.14824.667450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.924151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4041536
X-RAY DIFFRACTIONr_chiral_restr0.0980.21668
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212264
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022094
X-RAY DIFFRACTIONr_nbd_refined0.2580.22819
X-RAY DIFFRACTIONr_nbd_other0.2080.210198
X-RAY DIFFRACTIONr_nbtor_refined0.1960.25501
X-RAY DIFFRACTIONr_nbtor_other0.0910.26100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.85237238
X-RAY DIFFRACTIONr_mcbond_other0.43432778
X-RAY DIFFRACTIONr_mcangle_it4.117511388
X-RAY DIFFRACTIONr_scbond_it5.96484557
X-RAY DIFFRACTIONr_scangle_it8.477113816
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Number: 3467 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Atight positional0.020.05
12Btight positional0.020.05
13Ctight positional0.020.05
14Dtight positional0.020.05
15Etight positional0.020.05
16Ftight positional0.020.05
21Atight positional0.020.05
22Btight positional0.020.05
23Ctight positional0.020.05
24Dtight positional0.020.05
25Etight positional0.020.05
26Ftight positional0.020.05
11Atight thermal0.070.5
12Btight thermal0.070.5
13Ctight thermal0.070.5
14Dtight thermal0.070.5
15Etight thermal0.060.5
16Ftight thermal0.060.5
21Atight thermal0.070.5
22Btight thermal0.070.5
23Ctight thermal0.070.5
24Dtight thermal0.070.5
25Etight thermal0.060.5
26Ftight thermal0.060.5
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 253 -
Rwork0.327 5156 -
obs--98.69 %
Refinement TLS params.Method: refined / Origin x: 23.3848 Å / Origin y: 39.4476 Å / Origin z: 38.6855 Å
111213212223313233
T0.1192 Å2-0.0727 Å20.0046 Å2-0.0998 Å2-0.0016 Å2--0.1095 Å2
L0.0087 °20.0148 °20.0377 °2-0.0253 °20.0642 °2--0.163 °2
S-0.05 Å °0.0121 Å °0.0099 Å °-0.0497 Å °0.0383 Å °0.0659 Å °0.0411 Å °0.0291 Å °0.0116 Å °

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