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- PDB-5zrt: Crystal structure of human C1ORF123 protein -

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Basic information

Entry
Database: PDB / ID: 5zrt
TitleCrystal structure of human C1ORF123 protein
ComponentsUPF0587 protein C1orf123
KeywordsUNKNOWN FUNCTION / human hypothetical protein
Function / homologyCXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / zinc ion binding / BETA-MERCAPTOETHANOL / CXXC motif containing zinc binding protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRahaman, S.N.A. / Yusop, J.M. / Mohamed-Hussein, Z.A. / Wan Mohd, A. / Ho, K.L. / Teh, A.H. / Waterman, J. / Ng, C.L.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Ministry of Science, Technology and Innovation (Malaysia)02-01-02-SF0993 (Ministry of Science, Technology and Innovation) Malaysia
Citation
Journal: Peerj / Year: 2018
Title: Crystal structure and functional analysis of human C1ORF123.
Authors: A Rahaman, S.N. / Mat Yusop, J. / Mohamed-Hussein, Z.A. / Aizat, W.M. / Ho, K.L. / Teh, A.H. / Waterman, J. / Tan, B.K. / Tan, H.L. / Li, A.Y. / Chen, E.S. / Ng, C.L.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Cloning, expression, purification, crystallization and X-ray crystallographic analysis of recombinant human C1ORF123 protein
Authors: Rhaman, S.N. / Yusop, M.J. / Mohamed-Hussein, Z.A. / Ho, K.L. / Teh, A.H. / Waterman, J. / Ng, C.L.
History
DepositionApr 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_volume ..._audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0587 protein C1orf123
B: UPF0587 protein C1orf123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,31213
Polymers40,4802
Non-polymers83211
Water3,225179
1
A: UPF0587 protein C1orf123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7878
Polymers20,2401
Non-polymers5477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area8420 Å2
MethodPISA
2
B: UPF0587 protein C1orf123
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5255
Polymers20,2401
Non-polymers2854
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-1 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.320, 65.350, 95.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 0 / Auth seq-ID: 1 - 160 / Label seq-ID: 21 - 180

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UPF0587 protein C1orf123


Mass: 20239.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1orf123 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NWV4

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Non-polymers , 5 types, 190 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.28 Å3/Da / Density % sol: 45.95 % / Description: Long rod
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M magnesium chloride hexahydrate, 0.1M sodium citrate tribasic buffer pH 6.5, 20% polyethylene glycol 3350
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→30.9 Å / Num. obs: 29180 / % possible obs: 98.1 % / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.065 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 10058 / Rsym value: 0.526 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZSO

1zso


Resolution: 1.9→30.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.102 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 1491 5.1 %RANDOM
Rwork0.1754 ---
obs0.1778 27649 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.73 Å2 / Biso mean: 46.861 Å2 / Biso min: 20.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.9→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 0 44 179 2748
Biso mean--66.48 50.61 -
Num. residues----320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022624
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9643528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0425326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2225.591127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57715477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5961512
X-RAY DIFFRACTIONr_chiral_restr0.1720.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021970
Refine LS restraints NCS

Ens-ID: 1 / Number: 185 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 112 -
Rwork0.232 1967 -
all-2079 -
obs--96.79 %
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)
10.537-0.13360.2671.95690.47011.21630.04240.0505-0.1073-0.0677-0.13020.29150.0486-0.18410.08790.06180.004-0.02680.0457-0.04020.0661-8.6603-13.585913.5771
23.88930.1897-0.58612.84550.5732.17910.0616-0.15180.5134-0.2882-0.12610.4318-0.3661-0.30.06460.14720.1005-0.07310.0854-0.06540.1411-13.556413.389814.3659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 160
2X-RAY DIFFRACTION2B1 - 160

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