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- PDB-5tf2: CRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGUL... -

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Basic information

Entry
Database: PDB / ID: 5tf2
TitleCRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN
ComponentsProlactin regulatory element-binding protein
KeywordsTRANSCRIPTION / WD40 / Activator / Protein Transport / Structural Genomics Consortium (SGC)
Function / homology
Function and homology information


regulation of COPII vesicle coating / : / protein exit from endoplasmic reticulum / COPII vesicle coating / XBP1(S) activates chaperone genes / Cargo concentration in the ER / COPII-mediated vesicle transport / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site ...regulation of COPII vesicle coating / : / protein exit from endoplasmic reticulum / COPII vesicle coating / XBP1(S) activates chaperone genes / Cargo concentration in the ER / COPII-mediated vesicle transport / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / GTPase activator activity / guanyl-nucleotide exchange factor activity / GTPase binding / endoplasmic reticulum membrane / DNA binding / membrane / nucleus
Similarity search - Function
Guanine nucleotide-exchange factor Sec12-like / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...Guanine nucleotide-exchange factor Sec12-like / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Prolactin regulatory element-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWalker, J.R. / Zhang, Q. / Dong, A. / Wernimont, A. / Li, Y. / He, H. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...Walker, J.R. / Zhang, Q. / Dong, A. / Wernimont, A. / Li, Y. / He, H. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Chen, Z. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: CRYSTAL STRUCTURE OF THE WD40 DOMAIN OF THE HUMAN PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN (CASP target)
Authors: Walker, J.R. / Zhang, Q. / Dong, A. / Wernimont, A. / Li, Y. / He, H. / Tempel, W. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Chen, Z. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionSep 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolactin regulatory element-binding protein


Theoretical massNumber of molelcules
Total (without water)44,6762
Polymers44,6761
Non-polymers01
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.708, 160.708, 83.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Prolactin regulatory element-binding protein / Mammalian guanine nucleotide exchange factor mSec12


Mass: 44675.523 Da / Num. of mol.: 1 / Fragment: WD40 DOMAIN, RESIDUES 1-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREB, SEC12 / Plasmid: pFBOH-MHL / Cell line (production host): SF9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9HCU5
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PREB protein was mixed with elastase at 1:1000 (w/w) ratio before setting up crystallization. Crystals were grown at 293 K using the sitting drop method by mixing 0.5 uL protein with 0.5 uL ...Details: PREB protein was mixed with elastase at 1:1000 (w/w) ratio before setting up crystallization. Crystals were grown at 293 K using the sitting drop method by mixing 0.5 uL protein with 0.5 uL well solution consisting of 1.4M Malonate, pH 7.0. The crystals were cryoprotected by immersion in Paratone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.92045 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92045 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16070 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.031 / Rrim(I) all: 0.111 / Χ2: 0.971 / Net I/av σ(I): 24 / Net I/σ(I): 6.3 / Num. measured all: 198545
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.912.70.7790.8981100
2.9-3.0212.70.5260.9461100
3.02-3.1512.70.3590.9721100
3.15-3.3212.70.2440.9861100
3.32-3.5312.50.1720.9911100
3.53-3.812.60.1280.9951100
3.8-4.1812.40.0960.9961100
4.18-4.7912.30.0730.9981100
4.79-6.03120.0760.9971100
6.03-5011.10.0460.999199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
BALBESphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ERJ

1erj


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 21.049 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.25
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 784 4.9 %RANDOM
Rwork0.1888 ---
obs0.19 15265 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.32 Å2 / Biso mean: 46.35 Å2 / Biso min: 24.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----1.64 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 1 20 2540
Biso mean--30 39.25 -
Num. residues----338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192602
X-RAY DIFFRACTIONr_bond_other_d0.0010.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.9593553
X-RAY DIFFRACTIONr_angle_other_deg0.84935547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6145339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63223.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8661514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
X-RAY DIFFRACTIONr_mcbond_it0.8042.9761362
X-RAY DIFFRACTIONr_mcbond_other0.8022.9751361
X-RAY DIFFRACTIONr_mcangle_it1.4824.4531699
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 63 -
Rwork0.263 1102 -
all-1165 -
obs--99.74 %
Refinement TLS params.Method: refined / Origin x: 99.5777 Å / Origin y: 61.3455 Å / Origin z: 8.8601 Å
111213212223313233
T0.0371 Å2-0.0324 Å2-0.0159 Å2-0.0915 Å20.0492 Å2--0.0486 Å2
L3.4355 °2-0.1053 °20.8192 °2-2.124 °20.1187 °2--1.6411 °2
S-0.1509 Å °-0.068 Å °0.1374 Å °-0.0578 Å °0.0503 Å °-0.0212 Å °-0.1386 Å °0.0445 Å °0.1006 Å °

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