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

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Basic information

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


membrane raft distribution / NAD(P)H-hydrate epimerase / NAD(P)HX 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 / NAD(P)HX 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 / identical protein binding / metal ion binding
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
THEOPHYLLINE / NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 26, 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: 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 1.3Sep 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1493
Polymers29,8731
Non-polymers2762
Water25214
1
A: Apolipoprotein A-I-binding protein
hetero molecules

A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2986
Polymers59,7462
Non-polymers5524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2800 Å2
ΔGint-16 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.849, 125.849, 116.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 29872.963 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
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: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 11, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionAv R equivalents: 0.089 / Number: 97986
ReflectionResolution: 2.35→50 Å / Num. all: 97986 / Num. obs: 97986 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 42.447
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 5.677 / Rsym value: 0.498 / % possible all: 100
Cell measurementReflection used: 97986

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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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.312 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 656 5 %RANDOM
Rwork0.177 ---
obs0.18 13237 94.43 %-
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 max: 147.34 Å2 / Biso mean: 66.322 Å2 / Biso min: 3.14 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0.92 Å20 Å2
2---1.85 Å20 Å2
3---2.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 18 14 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221877
X-RAY DIFFRACTIONr_bond_other_d0.0010.021274
X-RAY DIFFRACTIONr_angle_refined_deg1.7862.0052559
X-RAY DIFFRACTIONr_angle_other_deg0.96733133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5785232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.24924.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.16115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.908156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02351
X-RAY DIFFRACTIONr_mcbond_it0.7861.51169
X-RAY DIFFRACTIONr_mcbond_other0.1831.5460
X-RAY DIFFRACTIONr_mcangle_it1.44221900
X-RAY DIFFRACTIONr_scbond_it2.5853708
X-RAY DIFFRACTIONr_scangle_it3.9244.5659
LS refinement shellResolution: 2.401→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 57 -
Rwork0.231 962 -
all-1019 -
obs--98.93 %
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)
17.12685.2273-0.101217.4306-3.50126.18150.15570.4599-0.2598-3.0888-0.898-2.7461.1740.72740.74241.13850.47690.74120.30360.36010.75814.05228.61225.958
21.1636-0.1882-0.058813.1232-6.47084.23560.23950.00880.08530.5099-0.24680.0307-0.2729-0.03920.00730.3042-0.0702-0.05270.10450.02490.16383.39324.57246.033
33.1653-0.22180.627812.6515-3.05313.07040.22880.0145-0.0580.1918-1.1596-1.9242-0.04540.47040.93080.1964-0.0299-0.1450.17590.26030.508712.87418.22447.923
41.0929-0.32820.06438.8005-2.70485.22860.18450.1202-0.2068-2.1439-0.4154-0.58491.09380.27520.23080.76020.12180.09480.09370.05470.22747.99211.36835.708
52.62880.2822-0.495511.216-3.41353.64450.22890.17040.0063-2.6128-0.18160.23650.9242-0.3552-0.04730.9940.0048-0.14040.16290.05630.12640.98326.7826.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 55
2X-RAY DIFFRACTION2A56 - 109
3X-RAY DIFFRACTION3A110 - 162
4X-RAY DIFFRACTION4A163 - 214
5X-RAY DIFFRACTION5A215 - 258

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