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- PDB-3roe: Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in ... -

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Basic information

Entry
Database: PDB / ID: 3roe
TitleCrystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine
ComponentsApolipoprotein A-I-binding protein
KeywordsPROTEIN BINDING / ROSSMANN FOLD
Function / homology
Function and homology information


membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis ...membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis / cilium / cell body / nucleotide binding / mitochondrion / extracellular space / extracellular region / identical protein binding / metal ion binding
Similarity search - Function
YjeF N-terminal domain-containing protein NAXE-like / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE / NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsShumilin, I.A. / Jha, K.N. / Cymborowski, M. / Herr, J.C. / Minor, W.
CitationJournal: Structure / Year: 2012
Title: Identification of unknown protein function using metabolite cocktail screening.
Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _chem_comp.type ..._audit_author.identifier_ORCID / _chem_comp.type / _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 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)180,69112
Polymers179,2386
Non-polymers1,4536
Water8,593477
1
A: Apolipoprotein A-I-binding protein
C: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2304
Polymers59,7462
Non-polymers4842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-20 kcal/mol
Surface area18840 Å2
MethodPISA
2
B: Apolipoprotein A-I-binding protein
D: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2304
Polymers59,7462
Non-polymers4842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-18 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)60,2304
Polymers59,7462
Non-polymers4842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-18 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.209, 124.446, 164.249
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Apolipoprotein A-I-binding protein / AI-BP


Mass: 29872.963 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aibp, Apoa1bp / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4Z3
#2: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N2O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, 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: 21-ID-D / Wavelength: 1.12712 Å
DetectorType: MARMOSAIC 300 / Detector: CCD / Date: Nov 22, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionAv R equivalents: 0.087 / Number: 477756
ReflectionResolution: 2.11→50 Å / Num. all: 477756 / Num. obs: 477756 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 26.826
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.568 / Rsym value: 0.593 / % possible all: 83.3
Cell measurementReflection used: 477756

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O8N

2o8n


Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.572 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 5864 5 %RANDOM
Rwork0.17651 ---
obs0.17823 111053 97.8 %-
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: 34.638 Å2
Baniso -1Baniso -2Baniso -3
1-5.04 Å20 Å24.49 Å2
2---3.5 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10848 0 102 477 11427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211274
X-RAY DIFFRACTIONr_bond_other_d00.027693
X-RAY DIFFRACTIONr_angle_refined_deg1.732.00515368
X-RAY DIFFRACTIONr_angle_other_deg4.049318933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22451396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67624.678451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.741151809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2951536
X-RAY DIFFRACTIONr_chiral_restr0.1050.21689
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112366
X-RAY DIFFRACTIONr_gen_planes_other0.010.022108
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_it0.9441.57020
X-RAY DIFFRACTIONr_mcbond_other01.52762
X-RAY DIFFRACTIONr_mcangle_it1.694211412
X-RAY DIFFRACTIONr_scbond_it2.79734254
X-RAY DIFFRACTIONr_scangle_it4.3024.53954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 408 -
Rwork0.257 7719 -
obs--92.13 %
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)
11.39581.4255-0.02522.4689-0.22030.65970.1221-0.0844-0.09260.4068-0.0934-0.0259-0.05770.0171-0.02870.18550.0027-0.06520.19120.02740.1426-0.5760.27390.997
20.6841-0.51080.07461.3556-0.14570.34140.07730.0404-0.0704-0.121-0.04970.01430.00890.0179-0.02760.07560.0256-0.15820.302-0.0080.232752.5054.067148.605
32.12071.921-0.56842.7018-0.79330.94970.09030.14620.32090.14010.17970.4293-0.1432-0.0251-0.270.1375-0.0086-0.06730.19640.03850.19098.57226.23978.596
41.148-0.739-0.07851.01250.21410.4664-0.0063-0.05650.07130.01220.0306-0.086-0.0681-0.0028-0.02430.07120.03-0.1430.3034-0.01410.213144.23430.453160.798
50.7076-0.0572-0.77590.5636-0.11662.2272-0.0458-0.038-0.0334-0.1002-0.0231-0.04360.0520.13850.06890.0910.0083-0.11270.2770.00910.144435.82633.618109.475
61.1472-0.4271-0.71020.52650.40072.0484-0.07080.0525-0.16980.0091-0.02590.11060.0736-0.21990.09660.0666-0.0006-0.13560.3085-0.01420.218114.63935.349130.991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 258
2X-RAY DIFFRACTION2B26 - 258
3X-RAY DIFFRACTION3C26 - 258
4X-RAY DIFFRACTION4D26 - 258
5X-RAY DIFFRACTION5E26 - 258
6X-RAY DIFFRACTION6F26 - 258

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