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- PDB-5kkp: Crystal Structure of Human Pseudouridylate Synthase 7 -

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Basic information

Entry
Database: PDB / ID: 5kkp
TitleCrystal Structure of Human Pseudouridylate Synthase 7
ComponentsPseudouridylate synthase 7
KeywordsISOMERASE / PUS7 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of mesoderm development / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / regulation of hematopoietic stem cell differentiation / negative regulation of translation / enzyme binding ...regulation of mesoderm development / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / regulation of hematopoietic stem cell differentiation / negative regulation of translation / enzyme binding / RNA binding / nucleus
Similarity search - Function
Pseudouridine synthase TruD, conserved site / tRNA pseudouridine synthase D (TruD) / Uncharacterized protein family UPF0024 signature. / Pseudouridine synthase, TruD, insertion domain / TRUD domain profile. / Pseudouridine synthase, TruD, catalytic domain / Pseudouridine synthase, TruD / Pseudouridine synthase, catalytic domain superfamily
Similarity search - Domain/homology
Pseudouridylate synthase 7 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsDONG, A. / ZENG, H. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal Structure of Human Pseudouridylate Synthase 7
Authors: ZENG, H. / DONG, A. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pseudouridylate synthase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3115
Polymers65,2491
Non-polymers624
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.356, 73.400, 138.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pseudouridylate synthase 7 /


Mass: 65249.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PUS7, KIAA1897 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL
References: UniProt: Q96PZ0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 23% PEG 3350, 0.2 M Sodium formate, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97901 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 27643 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 54.91 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.028 / Rrim(I) all: 0.105 / Χ2: 1.856 / Net I/av σ(I): 34.267 / Net I/σ(I): 6.9 / Num. measured all: 364318
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.26-2.38.80.823195.3
2.3-2.349.90.781197.9
2.34-2.3910.90.711199.4
2.39-2.4312.20.642199.6
2.43-2.4913.10.62199.8
2.49-2.5513.40.521199.8
2.55-2.6113.60.458199.9
2.61-2.6813.80.391100
2.68-2.7613.90.311100
2.76-2.85140.2491100
2.85-2.9514.10.217199.9
2.95-3.0714.10.1681100
3.07-3.2114.20.141100
3.21-3.3814.30.1091100
3.38-3.5914.30.0931100
3.59-3.8614.40.0831100
3.86-4.2514.40.0761100
4.25-4.8714.10.0671100
4.87-6.1313.80.071100
6.13-5012.10.074199.9

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.2refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
Cootmodel building
HKL-3000data reduction
RESOLVEphasing
WARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.26→27.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.275 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.226
Details: Due to ambiguous electron density, it is possible the region from residue 163 to 178 may be assigned to the sequence incorrectly.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 695 2.52 %RANDOM
Rwork0.209 ---
obs0.21 27570 98.8 %-
Displacement parametersBiso max: 161.37 Å2 / Biso mean: 59.6 Å2 / Biso min: 28.35 Å2
Baniso -1Baniso -2Baniso -3
1--6.9025 Å20 Å20 Å2
2--0.4189 Å20 Å2
3---6.4835 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.26→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 7 82 3988
Biso mean--54.92 52.51 -
Num. residues----509
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1363SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes594HARMONIC5
X-RAY DIFFRACTIONt_it4026HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion540SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4486SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4026HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5462HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion17.11
LS refinement shellResolution: 2.25→2.33 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.268 58 2.29 %
Rwork0.224 2476 -
all-2534 -
obs--88.68 %
Refinement TLS params.Method: refined / Origin x: 32.2466 Å / Origin y: 53.2764 Å / Origin z: 17.303 Å
111213212223313233
T-0.1029 Å20.0141 Å2-0.0296 Å2--0.1281 Å20.0136 Å2---0.1637 Å2
L0.6458 °2-0.1872 °2-0.498 °2-1.1243 °20.0972 °2--1.1127 °2
S0.0413 Å °0.0934 Å °0.0366 Å °-0.0611 Å °0.0234 Å °-0.0901 Å °-0.0252 Å °0.0027 Å °-0.0647 Å °
Refinement TLS groupSelection details: { A|* }

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