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- PDB-6q10: Crystal structure of the soluble domain (residues 71-217) of a co... -

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Basic information

Entry
Database: PDB / ID: 6q10
TitleCrystal structure of the soluble domain (residues 71-217) of a conserved hypothetical secreted protein (Rv2700 ortholog) from Mycobacterium marinum
ComponentsMymaA.19257.a.B3
KeywordsUNKNOWN FUNCTION / SSGCID / Mycobacerium marinum / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / secreted protein / Rv2700 ortholog
Function / homologyLytR/CpsA/Psr regulator, C-terminal domain / LytR cell envelope-related transcriptional attenuator / membrane / Conserved hypothetical secreted protein
Function and homology information
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: SSGCID, Mycobacerium marinum, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, secreted protein, Rv2700 ortholog
Authors: Phan, J.N. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MymaA.19257.a.B3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4633
Polymers16,3391
Non-polymers1242
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 46.570, 69.570
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 MymaA.19257.a.B3


Mass: 16339.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_2014
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B2HM00
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Hampton Research Index screen, condition H1 (305884h1): 100mM Citric acid pH 3.5, 2000mM Ammonium sulfate: MymaA.19257.a.B3.PS38530 at 22.5mg/ml cryo: 25% EG: tray 305841 H1: puck bqx9-4. ...Details: Hampton Research Index screen, condition H1 (305884h1): 100mM Citric acid pH 3.5, 2000mM Ammonium sulfate: MymaA.19257.a.B3.PS38530 at 22.5mg/ml cryo: 25% EG: tray 305841 H1: puck bqx9-4. For experimental phasing, a crystal from the same condition, Index H1 (305884h1), was soaked for 15 seconds each in a mix of 87.5% reservoir / 12.5% 2.5M sodium iodide in ethylene glycol, followed by a soak in 75% reservoir / 25% 2.5M sodium iodide in ethylene glycol, vitrified in liquid nitrogen for in-house data collection at Cu-Kalpha wavelength: puck vgz4-3

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDApr 11, 2019
RIGAKU SATURN 944+2CCDApr 18, 2019
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1C(111)SINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.6→38.7 Å / Num. obs: 18638 / % possible obs: 99.1 % / Redundancy: 6.683 % / Biso Wilson estimate: 31.596 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.031 / Χ2: 1.03 / Net I/σ(I): 31.67 / Num. measured all: 124550 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.644.3440.3483.455417135812470.9010.39591.8
1.64-1.695.0430.3034.556546132912980.9250.33897.7
1.69-1.746.360.2496.788363131513150.9690.271100
1.74-1.797.2460.18310.239007124512430.9860.19799.8
1.79-1.857.2730.14312.938873122112200.9920.15499.9
1.85-1.917.2740.10916.518576117911790.9950.117100
1.91-1.987.260.07722.588255113711370.9980.083100
1.98-2.077.2440.06228.057860108610850.9980.06799.9
2.07-2.167.1920.04934.497739107810760.9990.05299.8
2.16-2.267.1740.04238.917310101910190.9990.046100
2.26-2.397.1660.03843.7169519739700.9990.04199.7
2.39-2.537.0950.03347.6265279229200.9990.03699.8
2.53-2.77.0360.02953.0260658628620.9990.032100
2.7-2.926.990.02756.7557048178160.9990.02999.9
2.92-3.26.8870.02560.64513174574510.027100
3.2-3.586.7570.02265.77466269169010.02499.9
3.58-4.136.7350.02168.3411561161110.023100
4.13-5.066.5770.0269.3834795295290.9990.022100
5.06-7.166.3270.01966.24268942642510.02199.8
7.16-38.75.1040.02259.9312812632510.9990.02495.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_3500refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→38.7 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.25
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1866 10.04 %0
Rwork0.17 ---
obs0.1731 18589 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.09 Å2 / Biso mean: 31.2634 Å2 / Biso min: 15.62 Å2
Refinement stepCycle: final / Resolution: 1.6→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 8 125 1191
Biso mean--44.14 43.48 -
Num. residues----148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081101
X-RAY DIFFRACTIONf_angle_d1.0271510
X-RAY DIFFRACTIONf_dihedral_angle_d9.71672
X-RAY DIFFRACTIONf_chiral_restr0.063182
X-RAY DIFFRACTIONf_plane_restr0.007206
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6001-1.64330.26341420.2286117292
1.6433-1.69170.26941330.2115124598
1.6917-1.74630.25121530.19011263100
1.7463-1.80870.19391220.18381284100
1.8087-1.88110.22791400.18151291100
1.8811-1.96670.18621600.16971264100
1.9667-2.07040.20711490.16841265100
2.0704-2.20010.2121380.16941298100
2.2001-2.36990.19211310.17391312100
2.3699-2.60840.20241540.17341294100
2.6084-2.98570.21741540.18171294100
2.9857-3.76120.18311300.16551346100
3.7612-38.70.19751600.1561139599
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)
17.0226-2.46433.27462.1463-1.93194.318-0.2242-0.62160.15330.31930.23840.0655-0.4629-0.5479-0.06960.25250.03110.01910.22470.01490.184910.49552.168612.8222
26.0330.7092-0.40732.73330.14312.38350.0646-0.322-0.22940.01180.30360.3061-0.1608-0.6148-0.24080.24020.023-0.0490.27320.1180.27368.182755.18643.5794
35.3441-5.90845.32986.895-5.4145.99570.35470.38060.4601-0.16-0.466-0.5404-0.10060.3038-0.00360.3107-0.00840.06470.27350.06850.312824.685350.6310.5608
44.5029-1.53533.06182.7487-1.85954.57110.0198-0.4631-0.4120.19440.20750.19250.1222-0.4029-0.21020.1783-0.01970.0110.21040.05630.201214.481640.512413.776
54.3728-1.5415-0.48454.1556-0.78562.6663-0.0229-0.07910.03220.0671-0.0392-0.41550.01210.21120.06280.1322-0.0012-0.00080.11870.02550.171623.187844.12168.2873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 177 through 196 )A177 - 196
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 217 )A197 - 217
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 83 )A70 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 125 )A84 - 125
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 176 )A126 - 176

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