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- PDB-3e0z: Crystal structure of a putative imidazole glycerol phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 3e0z
TitleCrystal structure of a putative imidazole glycerol phosphate synthase homolog (eubrec_1070) from eubacterium rectale at 1.75 A resolution
Componentsprotein of unknown function
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyDomain of unknown function DUF3837 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (RER070207001348) from Eubacterium rectale at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein of unknown function
B: protein of unknown function
C: protein of unknown function
D: protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2208
Polymers50,7084
Non-polymers5134
Water7,098394
1
A: protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8893
Polymers12,6771
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7832
Polymers12,6771
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8712
Polymers12,6771
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: protein of unknown function


Theoretical massNumber of molelcules
Total (without water)12,6771
Polymers12,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.790, 60.180, 59.860
Angle α, β, γ (deg.)90.000, 98.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 3 - 105 / Label seq-ID: 4 - 106

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
protein of unknown function


Mass: 12676.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Gene: RER070207001348 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.82 Å3/Da / Density % sol: 32.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30.0000% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97895
SYNCHROTRONSSRL BL11-120.97872, 0.97931, 0.91837
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJun 15, 2008Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDJun 23, 2008Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.978721
30.979311
40.918371
ReflectionResolution: 1.75→29.656 Å / Num. obs: 36433 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.79 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.82.50.5371.4666626600.53797.7
1.8-1.842.70.4871.6720826230.48797.9
1.84-1.94.80.4931.51190924900.49398.5
1.9-1.964.80.4021.91160824350.40298.5
1.96-2.024.80.3272.31156824120.32798.8
2.02-2.094.80.2852.51095823000.28598.8
2.09-2.174.80.2263.31059922270.22699
2.17-2.264.70.2193.21031121740.21999.1
2.26-2.364.80.1824.1985620650.18299.1
2.36-2.474.80.1664.3941019580.16699.3
2.47-2.614.80.1484.9912619070.14899.4
2.61-2.774.80.145848317680.1499.4
2.77-2.964.80.1175.8807416930.11799.6
2.96-3.24.80.1036.4759115890.10399.6
3.2-3.54.70.0857.4684214480.08599.8
3.5-3.914.70.0698.3617913040.06999.7
3.91-4.524.70.0678.2552511740.06799.7
4.52-5.534.70.0697.746689950.06999.9
5.53-7.834.60.0717.635487750.07199.9
7.83-29.664.30.0557.518964360.05598.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.656 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.559 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.133
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PEG MOLECULES FROM CRYOPROTECTION CONDITIOIN ARE MODELED INTO THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1801 5 %RANDOM
Rwork0.171 ---
obs0.174 36334 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20.13 Å2
2--1.07 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 34 394 3859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223661
X-RAY DIFFRACTIONr_bond_other_d0.0050.022406
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9674967
X-RAY DIFFRACTIONr_angle_other_deg1.6135959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7415457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22826.092174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.71915661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.333158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024088
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02656
X-RAY DIFFRACTIONr_nbd_refined0.1790.3794
X-RAY DIFFRACTIONr_nbd_other0.1140.32620
X-RAY DIFFRACTIONr_nbtor_refined0.1580.51797
X-RAY DIFFRACTIONr_nbtor_other0.0820.51692
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5521
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0850.327
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.359
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.576
X-RAY DIFFRACTIONr_mcbond_it1.6232367
X-RAY DIFFRACTIONr_mcbond_other0.5783895
X-RAY DIFFRACTIONr_mcangle_it2.08853633
X-RAY DIFFRACTIONr_scbond_it3.97181530
X-RAY DIFFRACTIONr_scangle_it5.404111334
Refine LS restraints NCS

Ens-ID: 1 / Number: 1240 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.480.5
2BMEDIUM POSITIONAL0.380.5
3CMEDIUM POSITIONAL0.440.5
4DMEDIUM POSITIONAL0.530.5
1AMEDIUM THERMAL0.862
2BMEDIUM THERMAL1.072
3CMEDIUM THERMAL0.992
4DMEDIUM THERMAL0.92
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 118 -
Rwork0.206 2545 -
all-2663 -
obs--97.98 %
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)
10.4083-0.0607-0.06560.77510.0840.34950.01940.0164-0.015-0.0713-0.0076-0.02050.00820.006-0.0118-0.0134-0.00430.0055-0.0129-0.0055-0.013236.088510.348420.1261
20.53140.3412-0.28640.87790.16960.47380.059-0.0030.0211-0.0669-0.04840.0174-0.0796-0.0482-0.0107-0.00760.00690.0055-0.02070.0053-0.010210.588310.751420.2696
31.01450.0315-0.12920.3175-0.38170.90990.0214-0.0394-0.0350.0165-0.02040.0092-0.00660.1027-0.001-0.0146-0.00070.0008-0.00690.004-0.019121.196811.1709-8.7057
40.5283-0.16840.01740.3869-0.30320.5769-0.0009-0.0229-0.03250.00490.0151-0.00240.00360.0301-0.0141-0.0142-0.0078-0.008-0.0026-0.0026-0.011446.798311.4711-9.0249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1061 - 107
2X-RAY DIFFRACTION2BB1 - 1082 - 109
3X-RAY DIFFRACTION3CC0 - 1071 - 108
4X-RAY DIFFRACTION4DD0 - 1071 - 108

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