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- PDB-7tcb: Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio ... -

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Basic information

Entry
Database: PDB / ID: 7tcb
TitleCrystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus
ComponentsYaeQ family protein VPA0551
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyYaeQ / YaeQ superfamily / YaeQ protein / YaeQ / Restriction endonuclease type II-like / Cellulose synthase operon C protein
Function and homology information
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKim, Y. / Mulligan, R. / Maltseva, N. / Gu, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the YaeQ Family Protein VPA0551 from Vibrio parahaemolyticus
Authors: Kim, Y. / Mulligan, R. / Maltseva, N. / Gu, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YaeQ family protein VPA0551
B: YaeQ family protein VPA0551
C: YaeQ family protein VPA0551
D: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)85,5014
Polymers85,5014
Non-polymers00
Water1629
1
A: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: YaeQ family protein VPA0551


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.024, 47.687, 115.519
Angle α, β, γ (deg.)90.000, 99.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
YaeQ family protein VPA0551


Mass: 21375.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Strain: RIMD 2210633 / Gene: VPA0551 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q87IQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 24176 / % possible obs: 95.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 76.65 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.124 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 844 / CC1/2: 0.621 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.92 Å / SU ML: 0.4229 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 1140 4.78 %
Rwork0.2235 22706 -
obs0.2253 23846 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5609 0 0 9 5618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185747
X-RAY DIFFRACTIONf_angle_d0.43947790
X-RAY DIFFRACTIONf_chiral_restr0.0428868
X-RAY DIFFRACTIONf_plane_restr0.0035989
X-RAY DIFFRACTIONf_dihedral_angle_d13.88742138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.820.38881100.35852232X-RAY DIFFRACTION75.06
2.82-2.970.3991350.33682652X-RAY DIFFRACTION90.31
2.97-3.160.3251590.30362895X-RAY DIFFRACTION99.22
3.16-3.40.31061630.27132934X-RAY DIFFRACTION99.84
3.4-3.740.27741320.2472964X-RAY DIFFRACTION99.9
3.74-4.280.28791520.21042971X-RAY DIFFRACTION99.84
4.29-5.40.22841370.18223001X-RAY DIFFRACTION100
5.4-40.920.22391520.20143057X-RAY DIFFRACTION98.62
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)
15.04161430374-0.931945769837-0.6181937744566.814068021012.691188094993.473314970750.0008766893598270.464419296223-0.5652048981810.923399568929-0.3090772837010.5603954467820.80914098435-0.381514791808-0.1175171683570.7342127189020.0407561927057-0.04021621450.5543088441370.03575164738060.705247466323-3.40259091241-7.6747447928993.6933940634
27.78798709382-1.941180098413.36431467030.540426415258-0.9406750273891.56764690483-0.1635865745371.55722145149-0.801478465718-0.452997234074-0.01776168179440.4954956730770.970497158865-0.46753554424-0.03682928107490.791666045076-0.104411965549-0.01195272776450.739230043296-0.08547367738730.716065983061-5.88207308924-5.9902071885783.1847979659
34.804382412042.0710614441-1.868803091355.49287621848-0.5892089877276.56284248404-0.1189633363770.543887132757-0.0422464702871-0.899546360760.05986981992950.7872435198840.169048692079-0.7732669362420.142839464870.875366097817-0.0309578413801-0.09554071139850.880739396125-0.05245000065720.57122315502-13.84531435580.56898936459878.8396530917
41.91687911651-2.103175629632.196904192374.36513253064-1.682788818995.29475273216-0.1002572509620.2706268345050.0819435695823-1.061603108820.0030490261353-0.2825630075670.3056516120950.4844968184930.1074697239640.733553568627-0.06869770853330.008368022378030.9473163002910.1549009217380.645393294188-0.685833007294.3797426619482.8939537904
54.497687435950.254394475482-2.727902143027.535765315613.431584434425.65048256496-0.601470052529-0.6312992547430.7233300746690.08434862404090.452086211615-0.772431220391-0.166791085086-0.221678145496-0.08382900168580.687603457432-0.06345514397170.0877712243950.8361054642910.01316785595680.3540442800120.6767082661095.8623668405991.1528363244
63.576294832440.3297791321955.016270276684.624504674640.2109205183567.632085839940.377355742759-1.68414050720.2340737499750.488555277863-0.124633893639-0.473380808914-0.546232187498-1.21794249112-0.2136143721690.6832653404550.05608254451510.2146313154081.39935228259-0.2149173197571.12969211289-13.3897103329-28.0247980108123.521009675
75.642044032581.72165469595-3.077412901762.9077891926-2.358638043815.419558187420.364922596488-0.1952458799521.02476363664-0.3852682307890.02048914705050.310758198089-0.51301170739-0.350410856807-0.2730118176880.6382220514340.1187269462830.06877071888450.586933607435-0.02828069755170.813683020673-8.08925384311-25.6497841818111.976784505
84.39980955464-0.89543484221-0.8774575762267.36583879544-2.718115196656.625097140520.202017409621.77300854212.37291255734-2.724750110970.864366936926-0.3173506490140.516747488327-0.360547575163-0.485587305180.7413078122470.09616651668190.2473101727130.673208652460.1779890381321.186283409532.0515224068-24.114683785100.95890558
94.64187737560.32990132856-0.2166634214524.76240323465-1.133850141477.084889282220.0538498916908-0.107247373946-0.0137765216402-0.0687071258759-0.17381332457-0.1344851641730.7641146294240.5312847120890.2518788663940.5920863017720.0413182079484-0.05509619247180.4539181808420.0013683711390.5568687667280.0229248639028-36.6410778417111.226624881
101.44534384206-0.927984250267-0.719639288433.703978405810.9514827762756.086961421990.168532426839-1.338549254850.1827951814040.830212853706-0.264125899960.6944393501750.342251505004-0.471751935630.1846963405630.9396127857-0.0723387688212-0.04176977571891.394951738820.01966597007980.684985133496-6.95289942966-36.8622030432124.673301334
113.430719328730.546376266944-1.452562706359.43011232285-1.334329275954.125546603390.5432463225280.346754039245-0.208367495215-1.84021792827-0.597367622125-0.669195615153-0.1285088287172.41150092022-0.02016069731141.15158112859-0.2145555821750.1348460576552.01982586870.04744254264430.66989554570525.59568790140.99330984603158.9538246731
121.669043260971.299024053891.213225352982.768154863374.279647154426.73407302363-0.02319727891890.2649943418560.53050710347-1.18958111850.233155037270.0732019362528-1.544623608511.6317310257-0.1535084822551.26642269181-0.1615619926510.007345638984641.673046678980.09195724480080.6090438273817.55533698662.779180157851.5179418329
133.289530458783.106970568581.309584489453.212251494220.2329207538923.336671440961.086888554210.725558243703-1.04134304918-1.28271947682-0.388685511131-0.560768781951-0.2278800123311.22041801586-0.1195622091111.46125517813-0.0181865544491-0.03120587417941.72698052734-0.09706944828090.42875194172616.0544186341-5.0837128059943.8510318321
143.174687044650.01915068633840.4302861902391.93654329619-0.4152995521491.88840256321-0.9810876043320.911435059238-0.278944983078-1.676404934710.8446799505610.975809320559-0.6121648859480.881376042665-0.04154679503981.24588116586-0.12490853534-0.13662277181.3543633258-0.221529740320.6269354594337.49395238801-4.1174273841546.6300308035
151.743395035951.347402927391.506263397824.608830158130.5487110680254.63772239910.06886776180780.07750856384660.430270182875-1.118669329770.1351653879520.755387209701-0.606757428515-0.059393110014-0.1563954936270.9764613107680.0231608893556-0.09988339652381.49953561926-0.1266817750950.7412778775610.462465154946-5.157067888352.4777081989
164.74348843229-0.3919706289841.695544413063.04807475877-1.802854811954.999893514230.194359798052-0.1026679705730.410091846170.149867713655-0.385580776870.0990957910018-0.9496233210610.4374518324940.1464653126680.828675950686-0.0171865830119-0.000673832418411.1867346102-0.02002997496210.48429514496616.02699645971.7853826857665.6030436151
176.56460536546-2.327303586151.404203864343.591818169720.05495367637664.49013667389-0.183031492893-0.1814218404080.1566985418190.484084154048-0.048932063593-0.409633330118-0.009652053457280.6687279045760.3035418406810.682428083285-0.1809589621630.04671830303321.399465354780.1444636438220.52995171961432.5281343083-11.144537100984.8715499571
186.814926306340.330660392519-0.01967935071733.58515255754-1.76610025569.991749202280.0723822922366-0.591934473254-0.1822744075371.064461830550.0445119692193-0.569635005366-1.113912690750.895791119368-0.2003078154360.716227186745-0.0204993657344-0.05924418841890.9701793574330.008384061298110.58875418100523.515275707-14.744249162598.310386779
192.91142104272-0.5720556697340.2675832643014.63417720106-3.351071045786.213655136840.1403898889270.585411003775-0.176196690914-0.496069147492-0.253326867014-0.01593034436660.3903415755581.474092172860.1818871347370.6913040574740.0582489743188-0.03318663793361.08604570997-0.05871451737310.54919040126223.8904844043-20.560681249583.3644402568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 4 through 31 )CC4 - 311 - 28
22chain 'C' and (resid 32 through 68 )CC32 - 6829 - 62
33chain 'C' and (resid 69 through 110 )CC69 - 11063 - 104
44chain 'C' and (resid 111 through 155 )CC111 - 155105 - 149
55chain 'C' and (resid 156 through 179 )CC156 - 179150 - 173
66chain 'D' and (resid 3 through 31 )DD3 - 311 - 29
77chain 'D' and (resid 32 through 88 )DD32 - 8830 - 82
88chain 'D' and (resid 89 through 98 )DD89 - 9883 - 92
99chain 'D' and (resid 99 through 142 )DD99 - 14293 - 136
1010chain 'D' and (resid 143 through 178 )DD143 - 178137 - 172
1111chain 'A' and (resid 4 through 31 )AA4 - 311 - 28
1212chain 'A' and (resid 32 through 68 )AA32 - 6829 - 61
1313chain 'A' and (resid 69 through 88 )AA69 - 8862 - 81
1414chain 'A' and (resid 89 through 110 )AA89 - 11082 - 103
1515chain 'A' and (resid 111 through 133 )AA111 - 133104 - 126
1616chain 'A' and (resid 134 through 178 )AA134 - 178127 - 171
1717chain 'B' and (resid 3 through 49 )BB3 - 491 - 47
1818chain 'B' and (resid 50 through 98 )BB50 - 9848 - 93
1919chain 'B' and (resid 99 through 181 )BB99 - 18194 - 176

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