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

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Basic information

Entry
Database: PDB / ID: 3rog
TitleCrystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine 3'-monophosphate
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-3'-PHOSPHATE / NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: 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

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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)30,2913
Polymers29,8731
Non-polymers4182
Water1,06359
1
A: Apolipoprotein A-I-binding protein
hetero molecules

A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5826
Polymers59,7462
Non-polymers8374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2730 Å2
ΔGint-18 kcal/mol
Surface area18620 Å2
MethodPISA
2
A: Apolipoprotein A-I-binding protein
hetero molecules

A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5826
Polymers59,7462
Non-polymers8374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1630 Å2
ΔGint-7 kcal/mol
Surface area19720 Å2
MethodPISA
3
A: Apolipoprotein A-I-binding protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)181,74718
Polymers179,2386
Non-polymers2,51012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area9380 Å2
ΔGint-41 kcal/mol
Surface area54660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.094, 126.094, 110.962
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-T3P / THYMIDINE-3'-PHOSPHATE / ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
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: 1.04399 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 23, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04399 Å / Relative weight: 1
ReflectionAv R equivalents: 0.061 / Number: 119546
ReflectionResolution: 2.05→50 Å / Num. all: 119546 / Num. obs: 119546 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 38.741
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.203 / Rsym value: 0.361 / % possible all: 99.4
Cell measurementReflection used: 119546

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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: 2.05→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.857 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1089 5.1 %RANDOM
Rwork0.179 ---
obs0.18 21270 99.3 %-
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: 120.52 Å2 / Biso mean: 55.107 Å2 / Biso min: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1--4.54 Å2-2.27 Å20 Å2
2---4.54 Å20 Å2
3---6.81 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 26 59 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221885
X-RAY DIFFRACTIONr_bond_other_d00.021281
X-RAY DIFFRACTIONr_angle_refined_deg1.7522.012571
X-RAY DIFFRACTIONr_angle_other_deg4.04233152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6424.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56715301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.589156
X-RAY DIFFRACTIONr_chiral_restr0.110.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212058
X-RAY DIFFRACTIONr_gen_planes_other0.010.02351
X-RAY DIFFRACTIONr_mcbond_it0.9711.51169
X-RAY DIFFRACTIONr_mcbond_other01.5460
X-RAY DIFFRACTIONr_mcangle_it1.65821900
X-RAY DIFFRACTIONr_scbond_it2.8853716
X-RAY DIFFRACTIONr_scangle_it4.2384.5671
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 70 -
Rwork0.281 1432 -
all-1502 -
obs--95.06 %
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)
12.16411.67020.96451.90690.42111.23530.233-0.60180.24730.2377-0.25970.19820.0464-0.25760.02670.4017-0.07910.00690.5537-0.07790.146419.82522.28627.413
230.7182-1.177919.228733.93845.345723.98770.70010.9298-0.00430.6586-0.37910.14050.98451.0527-0.3210.35920.0048-0.00210.5144-0.12880.198322.6613.8745.375
32.85051.7471.07432.52720.08691.3514-0.0578-0.11940.3018-0.0324-0.03880.3292-0.0684-0.09380.09660.3631-0.0254-0.04990.3878-0.0090.164511.17619.25811.14
43.06661.50791.26021.72251.05931.77430.4221-0.7064-0.13720.3636-0.3391-0.04290.2852-0.3466-0.0830.4657-0.145-0.03480.55060.04110.071216.10212.41726.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 70
2X-RAY DIFFRACTION2A71 - 77
3X-RAY DIFFRACTION3A78 - 169
4X-RAY DIFFRACTION4A170 - 258

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