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- PDB-7lsq: The Crystal Structure of Q108K:K40E:T53A:R58W:Q38F:Q4F:Y19W Mutan... -

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Basic information

Entry
Database: PDB / ID: 7lsq
TitleThe Crystal Structure of Q108K:K40E:T53A:R58W:Q38F:Q4F:Y19W Mutant of HCRBPII Bound with LizFluor Chromophore Showing Excited State Intermolecular Proton Transfer
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / Domain Swapped Trimer / iLBP
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / Retinoid metabolism and transport / fatty acid transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin
Similarity search - Domain/homology
ACETATE ION / Chem-ZFG / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67130538298 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM101353 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase.
Authors: Santos, E.M. / Sheng, W. / Esmatpour Salmani, R. / Tahmasebi Nick, S. / Ghanbarpour, A. / Gholami, H. / Vasileiou, C. / Geiger, J.H. / Borhan, B.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
C: Retinol-binding protein 2
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,70212
Polymers62,6344
Non-polymers1,0678
Water7,062392
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9753
Polymers15,6591
Non-polymers3162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9753
Polymers15,6591
Non-polymers3162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9753
Polymers15,6591
Non-polymers3162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7773
Polymers15,6591
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.766, 54.99, 69.805
Angle α, β, γ (deg.)109.338, 97.797, 102.603
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 15658.552 Da / Num. of mol.: 4 / Mutation: Q4F, Y19W, Q38F, K40E, T53A, R58W, Q108K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P50120
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZFG / 4-{5-[(2E)-but-2-en-2-yl]thiophen-2-yl}-N,N-dimethylaniline


Mass: 257.394 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H19NS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: Ammonium acetate, PEG 4000, Sodium acetate / PH range: 4-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.671→34.9537 Å / Num. obs: 54659 / % possible obs: 96.4 % / Redundancy: 2.3 % / Biso Wilson estimate: 23.5108503086 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.7
Reflection shellResolution: 1.671→1.731 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.518 / Num. unique obs: 5195 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCT

2rct


Resolution: 1.67130538298→34.9535782641 Å / SU ML: 0.196712857991 / Cross valid method: FREE R-VALUE / σ(F): 1.96411700619 / Phase error: 24.8531031225
RfactorNum. reflection% reflection
Rfree0.2318796406 2026 3.70973943933 %
Rwork0.184544929343 52587 -
obs0.186257687006 54613 96.1970689777 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67130538298→34.9535782641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 74 392 4866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006944331901824706
X-RAY DIFFRACTIONf_angle_d1.052780555256382
X-RAY DIFFRACTIONf_chiral_restr0.044349772618671
X-RAY DIFFRACTIONf_plane_restr0.00392884578751822
X-RAY DIFFRACTIONf_dihedral_angle_d14.62885551141711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.71310.3230889933791540.2733254897413508X-RAY DIFFRACTION90.7558859975
1.7131-1.75940.2600189166251330.2379087209333671X-RAY DIFFRACTION94.5563012677
1.7594-1.81120.2580878078981370.2208129133683784X-RAY DIFFRACTION96.0088148874
1.8112-1.86960.258230424751460.2070402680453724X-RAY DIFFRACTION96.1251862891
1.8696-1.93650.2302828550531460.2004060997413839X-RAY DIFFRACTION96.3724304716
1.9365-2.0140.236290451521370.1914151547763710X-RAY DIFFRACTION96.5612449799
2.014-2.10560.2352016587861440.1896976727973810X-RAY DIFFRACTION96.9117647059
2.1056-2.21660.2321107970751430.1869368616433770X-RAY DIFFRACTION97.0004957858
2.2166-2.35550.2475090304211550.1946605762253801X-RAY DIFFRACTION97.0321314692
2.3555-2.53730.2327013368341400.1961025935933801X-RAY DIFFRACTION97.4771209498
2.5373-2.79250.2747379259261480.1982517768223843X-RAY DIFFRACTION97.6988984088
2.7925-3.19640.229690186191480.1934739951523780X-RAY DIFFRACTION97.493174485
3.1964-4.02620.225697994951470.1546146186653794X-RAY DIFFRACTION96.6405100539
4.0262-34.950.1963577152811480.1685785050513752X-RAY DIFFRACTION96.1301454277
Refinement TLS params.Method: refined / Origin x: 10.8803529356 Å / Origin y: -17.9030525751 Å / Origin z: 8.88895387344 Å
111213212223313233
T0.133803514275 Å20.0188985215328 Å20.00578636737645 Å2-0.159992834512 Å20.000456390370033 Å2--0.172549327258 Å2
L0.1951146462 °20.0454860214209 °2-0.0180623141567 °2-0.293217897696 °2-0.119283982546 °2--0.585931778747 °2
S0.0240210473717 Å °-0.0159811103657 Å °0.000207845702072 Å °-0.0271519578117 Å °-0.0477490945417 Å °-0.00522923451549 Å °-0.0302582213572 Å °-0.000724418066521 Å °0.0223071441421 Å °
Refinement TLS groupSelection details: all

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