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- PDB-5gml: Crystal Structure of GRASP Domain of GRASP55 with N terminal extr... -

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Basic information

Entry
Database: PDB / ID: 5gml
TitleCrystal Structure of GRASP Domain of GRASP55 with N terminal extra residues
ComponentsGolgi reassembly-stacking protein 2
KeywordsSTRUCTURAL PROTEIN / beta strand sandswish / classic PDZ peptide binding groove / conserved carboxylate-binding loop
Function / homology
Function and homology information


organelle organization / Golgi Cisternae Pericentriolar Stack Reorganization / establishment of protein localization to plasma membrane / organelle assembly / response to unfolded protein / response to endoplasmic reticulum stress / spermatogenesis / cell differentiation / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus
Similarity search - Function
GRASP55/65 / GRASP-type PDZ domain / GRASP55/65 PDZ-like domain / GRASP-type PDZ domain profile. / PDZ domain / Pdz3 Domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Golgi reassembly-stacking protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.546 Å
AuthorsShi, N. / Shi, X. / Morelli, X. / Betzi, S. / Huang, X.
Funding support China, France, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370738 China
Campus FrancePHC CAI YUANPEI 2013 - Project N26203WD France
CitationJournal: to be published
Title: Structural relationship of the tandem PDZ tandem from Grasp55 and its implication in the unconventional secretion pathway
Authors: Cartier-Michaud, A. / Betzi, S. / Shi, X. / Shi, N. / Morelli, X. / Aurrand-Lions, M.
History
DepositionJul 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2


Theoretical massNumber of molelcules
Total (without water)51,8902
Polymers51,8902
Non-polymers00
Water1,31573
1
A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2

A: Golgi reassembly-stacking protein 2
B: Golgi reassembly-stacking protein 2


Theoretical massNumber of molelcules
Total (without water)103,7804
Polymers103,7804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_575-x,-y+2,z1
Buried area14620 Å2
ΔGint-80 kcal/mol
Surface area35590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.312, 132.312, 221.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-328-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: -14 - 208 / Label seq-ID: 13 - 235

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Golgi reassembly-stacking protein 2 / GRS2 / Golgi reassembly-stacking protein of 55 kDa / GRASP55


Mass: 25945.014 Da / Num. of mol.: 2 / Fragment: grasp domain, UNP residues 2-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gorasp2,GOLPH6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99JX3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4.97 Å3/Da / Density % sol: 75.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: sodium formate, sodium acetate, etc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.546→93.56 Å / Num. obs: 32268 / % possible obs: 99.42 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.1306 / Net I/σ(I): 14.53
Reflection shellResolution: 2.546→2.637 Å / Redundancy: 14 % / Rmerge(I) obs: 0.9802 / Mean I/σ(I) obs: 3.57 / % possible all: 99.34

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
HKL-2000data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RLE

3rle


Resolution: 2.546→93.559 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3106 1887 6.18 %Random selection
Rwork0.261 57256 --
obs0.264 30510 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.08 Å2 / Biso mean: 66.6817 Å2 / Biso min: 22.79 Å2
Refinement stepCycle: final / Resolution: 2.546→93.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 73 3499
Biso mean---58.95 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083504
X-RAY DIFFRACTIONf_angle_d1.2614754
X-RAY DIFFRACTIONf_chiral_restr0.05520
X-RAY DIFFRACTIONf_plane_restr0.006624
X-RAY DIFFRACTIONf_dihedral_angle_d13.0121278
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1969X-RAY DIFFRACTION11.313TORSIONAL
12B1969X-RAY DIFFRACTION11.313TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5465-2.57870.40891400.32082070221098
2.5787-2.61270.3731440.324821162260100
2.6127-2.64850.3311370.292621362273100
2.6485-2.68630.33731450.305121672312100
2.6863-2.72640.35521380.301820912229100
2.7264-2.7690.34421410.289321422283100
2.769-2.81440.37591460.296921402286100
2.8144-2.86290.37391370.295421212258100
2.8629-2.9150.31781450.278821272272100
2.915-2.97110.3041400.278821402280100
2.9711-3.03170.33841350.268921502285100
3.0317-3.09760.40511400.271621082248100
3.0976-3.16970.26041400.254621422282100
3.1697-3.2490.3281400.246421142254100
3.249-3.33680.33831420.248121492291100
3.3368-3.4350.28211390.261121362275100
3.435-3.54590.27411390.253321352274100
3.5459-3.67260.27321430.242921232266100
3.6726-3.81970.30781430.247421522295100
3.8197-3.99350.26271340.244521032237100
3.9935-4.20410.29551430.246821272270100
4.2041-4.46750.33351380.227321492287100
4.4675-4.81240.26361360.236621282264100
4.8124-5.29660.30941410.246421482289100
5.2966-6.06290.27511410.27882114225599
6.0629-7.63810.34621430.260421322275100
7.6381-93.62190.33041230.29861896201989
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)
15.5259-1.1956-1.95424.4611.41650.9173-0.6657-0.3059-0.65450.51560.05990.66150.19820.24150.48630.45080.079-0.04770.3888-0.03020.403-12.666120.314175.3674
24.93595.0569-1.31885.1033-1.37470.32250.7079-0.75380.09470.77420.88721.5230.476-2.078-0.13610.5416-0.25940.12831.03910.54980.99894.5703106.047391.2032
33.2925-1.90162.61215.6545-1.43472.58220.2150.24530.11240.4881-0.0988-0.1236-0.3036-0.0573-0.04250.46380.05950.05960.4330.1790.415115.7976108.015287.3393
44.7559-0.69291.83943.8899-1.05062.16470.14340.3836-0.0213-0.0501-0.07660.20520.14710.1359-0.10430.37030.035-0.03490.35060.15630.540415.7953101.73987.5171
51.8371-0.98330.0995.24170.0623.01840.5285-0.29340.31050.3387-0.06380.3636-0.3716-0.2656-0.64120.5204-0.12020.05110.37350.15710.434718.0614110.768789.1511
65.72530.30981.47087.88120.42223.4080.1359-0.49110.00420.3663-0.1201-0.11020.03930.2184-0.1850.2930.07050.05810.41260.03250.222810.7587131.671881.4324
76.9389-4.51172.19213.40890.10445.6307-0.7448-1.5647-1.60782.37491.82630.4353-0.3687-0.5601-0.49781.27550.10990.2231.05650.2020.58747.8879130.892896.6755
84.14080.6908-0.84888.45521.48841.83220.0939-0.5147-0.06260.5236-0.0869-1.0131-0.3669-0.2396-0.01470.35270.0919-0.05130.58980.0830.357715.8816124.547384.0365
92.63732.12070.72365.03350.41823.0138-0.1235-0.33290.15220.10640.03910.3946-0.1534-0.0718-0.00350.24270.13310.06030.37790.0630.27065.7717129.227780.6652
105.6179-2.05590.45514.64330.48272.54040.1628-0.38790.9904-1.37230.5054-0.9486-0.34590.5553-0.42850.472-0.03540.22370.27040.13890.622112.2853145.048569.0444
116.175-1.2374-3.08842.22181.79495.76360.4646-0.19740.0901-0.1446-0.4573-0.1696-0.51370.5283-0.13850.4680.13870.12720.53780.05030.349522.8362119.051158.7814
123.874-2.2481-3.2143.54432.11152.20710.28420.34530.18-0.2627-0.0818-0.1409-0.12310.0783-0.17370.46890.24820.13210.64630.11770.420629.108117.893453.6867
134.9225-2.5453-0.50433.5508-0.55570.87320.1628-0.0381-0.19411.49180.03980.2041-0.9317-0.8795-0.2130.34761.00760.3388-0.00220.15560.677820.829114.355554.6891
145.6651-0.04770.13986.8990.96542.87890.51980.9042-0.3523-0.4438-0.6429-0.0288-0.0346-0.2010.2530.4770.2894-0.05440.5603-0.14850.36480.7098121.440562.2201
151.62072.39260.47078.65531.45650.24390.5741.3839-0.8710.22870.1827-1.3853-0.067-2.9901-0.91911.17770.3482-0.06051.9138-0.02860.83151.7387126.296847.8696
163.1434-1.0669-2.35994.267-0.46281.75150.51221.0281-0.5903-0.5207-0.61070.04180.1204-0.11030.04680.47070.3488-0.04560.7136-0.17940.32894.0807122.130761.0029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -14 through 5 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 19 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 20 through 53 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 85 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 86 through 109 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 110 through 139 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 160 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 161 through 178 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 179 through 208 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid -14 through 5 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 37 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 85 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 86 through 109 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 110 through 140 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 141 through 156 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 157 through 208 )B0

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