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- PDB-4uzr: Crystal Structure of Pyrococcus horikoshii Ph1500 -

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Basic information

Entry
Database: PDB / ID: 4uzr
TitleCrystal Structure of Pyrococcus horikoshii Ph1500
ComponentsPUTATIVE UNCHARACTERIZED PROTEIN PH1500
KeywordsUNKNOWN FUNCTION / BETA-PROPELLER / 12-BLADED / HEXAMER / DODECAMER / BETA-CLAM
Function / homology: / Domain of unknown function (DUF6849) / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / CDC48 domain-containing protein
Function and homology information
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.652 Å
AuthorsHartmann, M.D. / Ammelburg, M. / Djuranovic, S. / Lupas, A.N.
CitationJournal: To be Published
Title: Crystal Structure of Pyrococcus Horikoshii Ph1500
Authors: Ammelburg, M. / Schiff, J. / Hartmann, M.D. / Varnay, I. / Djuranovic, S. / Truffault, V. / Martin, J. / Coles, M. / Lupas, A.N.
History
DepositionSep 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
B: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
C: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
D: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
E: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
F: PUTATIVE UNCHARACTERIZED PROTEIN PH1500


Theoretical massNumber of molelcules
Total (without water)97,9826
Polymers97,9826
Non-polymers00
Water00
1
A: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
B: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
C: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
D: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
E: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
F: PUTATIVE UNCHARACTERIZED PROTEIN PH1500

A: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
B: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
C: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
D: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
E: PUTATIVE UNCHARACTERIZED PROTEIN PH1500
F: PUTATIVE UNCHARACTERIZED PROTEIN PH1500


Theoretical massNumber of molelcules
Total (without water)195,96312
Polymers195,96312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area41260 Å2
ΔGint-203.6 kcal/mol
Surface area69320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.779, 184.169, 172.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
PUTATIVE UNCHARACTERIZED PROTEIN PH1500


Mass: 16330.283 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: JCM 9974 / DSM 12428 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O59169

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP, 295 K, 30 %(V/V) PEG 400, 200 MM SODIUM CITRATE, 100 MM TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→39.1 Å / Num. obs: 28988 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.38 % / Biso Wilson estimate: 70.41 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.65→2.81 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.13 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.652→38.988 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1428 4.9 %
Rwork0.1996 --
obs0.2022 28970 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.652→38.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 0 0 6526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036604
X-RAY DIFFRACTIONf_angle_d0.89009
X-RAY DIFFRACTIONf_dihedral_angle_d14.1592465
X-RAY DIFFRACTIONf_chiral_restr0.0421188
X-RAY DIFFRACTIONf_plane_restr0.0041127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.652-2.74670.3741370.31742661X-RAY DIFFRACTION96
2.7467-2.85670.39611310.30022756X-RAY DIFFRACTION99
2.8567-2.98660.3611390.29032733X-RAY DIFFRACTION99
2.9866-3.1440.33751480.26952739X-RAY DIFFRACTION99
3.144-3.34090.33611420.2562737X-RAY DIFFRACTION100
3.3409-3.59870.27151460.2132741X-RAY DIFFRACTION99
3.5987-3.96050.26771410.20742746X-RAY DIFFRACTION99
3.9605-4.53290.22771440.16632747X-RAY DIFFRACTION98
4.5329-5.70810.1961470.15432791X-RAY DIFFRACTION98
5.7081-38.99210.20331530.17692891X-RAY DIFFRACTION98
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)
18.5611-6.2267-1.94818.09881.37257.3480.09250.4392-0.5501-0.0456-0.547-0.05452.06130.40980.47960.95360.1490.11140.564-0.03250.60210.696525.323258.271
23.5181.3276-0.83667.3262-2.42169.474-0.0209-0.1235-0.0016-0.3886-0.4158-0.25810.22170.50540.38170.4830.0774-0.02030.4684-0.04140.418115.652844.941133.3573
37.38751.00942.26936.81750.01445.385-0.0795-0.2814-0.09050.71710.0517-0.7109-0.18160.10330.0330.6590.0206-0.03280.4219-0.09120.43841.994797.927970.5068
45.69181.2393-1.1425.59450.07097.76310.0142-0.08780.2690.5041-0.1165-0.43240.44430.63580.08860.47060.1078-0.05790.42220.02940.391112.877965.97866.7514
59.42712.3374-0.75358.3709-0.43156.23390.12490.35030.13-0.5328-0.086-0.6018-0.45970.5138-0.05760.6797-0.0065-0.0420.33950.0630.30385.388972.20981.1816
63.6037-2.8107-2.09657.3177-0.58137.22910.270.11920.3202-0.49970.2038-0.6443-0.58070.6448-0.30460.5371-0.10820.00650.3539-0.00590.445815.210484.480231.1644
75.0043-0.84230.13915.83680.80035.7441-0.1996-0.4684-0.30571.1208-0.0397-0.27580.18440.07090.26480.4811-0.014-0.05580.34120.00060.3510.243652.283885.6666
80.9335-2.9915-3.44817.59838.38538.6686-0.4969-0.2142-0.20371.31150.2721-0.12491.4620.13980.19380.7570.10430.05520.5470.07760.461913.486645.717455.8616
93.7891-1.1229-2.5436.177-0.59947.77920.18690.11660.4213-0.11870.1739-0.1023-1.5279-0.0567-0.21680.7109-0.09080.03250.35910.06090.39342.3627107.933432.8939
101.7097-1.3334-2.55687.7587-3.60687.30310.0883-0.02760.00280.4317-0.2307-0.2494-0.69890.51170.1140.4698-0.0739-0.11080.37370.06710.479814.148985.060254.6621
114.79061.1702-0.5214.3194-3.2117.4642-0.05320.4064-0.4439-0.8945-0.2198-0.11561.4420.10460.23550.74440.06880.08030.2955-0.02270.45045.055134.547410.2871
121.17150.7036-0.99312.61690.57384.00430.17410.2066-0.326-1.0550.2468-0.448-0.06910.2734-0.3710.730.0224-0.04130.4869-0.07070.632516.615964.524221.517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 1:76)
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 77:148)
3X-RAY DIFFRACTION3(CHAIN B AND RESSEQ 1:76)
4X-RAY DIFFRACTION4(CHAIN B AND RESSEQ 77:148)
5X-RAY DIFFRACTION5(CHAIN C AND RESSEQ 1:76)
6X-RAY DIFFRACTION6(CHAIN C AND RESSEQ 77:148)
7X-RAY DIFFRACTION7(CHAIN D AND RESSEQ 1:76)
8X-RAY DIFFRACTION8(CHAIN D AND RESSEQ 77:148)
9X-RAY DIFFRACTION9(CHAIN E AND RESSEQ 1:76)
10X-RAY DIFFRACTION10(CHAIN E AND RESSEQ 77:148)
11X-RAY DIFFRACTION11(CHAIN F AND RESSEQ 1:76)
12X-RAY DIFFRACTION12(CHAIN F AND RESSEQ 77:148)

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