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- PDB-4e5v: Crystal structure of a Putative thua-like protein (PARMER_02418) ... -

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Basic information

Entry
Database: PDB / ID: 4e5v
TitleCrystal structure of a Putative thua-like protein (PARMER_02418) from Parabacteroides merdae ATCC 43184 at 1.75 A resolution
ComponentsPutative thua-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Thua-like proteins / trehalose utilisation / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyThuA-like domain / Trehalose utilisation / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / ThuA domain-containing protein
Function and homology information
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative thua-like protein (PARMER_02418) from Parabacteroides merdae ATCC 43184 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Putative thua-like protein
B: Putative thua-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,99420
Polymers63,8702
Non-polymers1,12418
Water11,548641
1
A: Putative thua-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4359
Polymers31,9351
Non-polymers5008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thua-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,55911
Polymers31,9351
Non-polymers62410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.590, 95.370, 70.600
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative thua-like protein


Mass: 31935.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_02418 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AG74
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
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 RESIDUES 25-304 OF 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: 2.19 Å3/Da / Density % sol: 43.96 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20.00% polyethylene glycol 3350, 0.200M ammonium fluoride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97941, 0.97882
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978821
ReflectionResolution: 1.75→29.832 Å / Num. obs: 51578 / % possible obs: 81.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.741 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.810.366210084849080.3
1.81-1.890.2662.711248948379
1.89-1.970.2013.59177779276.2
1.97-2.070.1534.210455887683.6
2.07-2.20.1125.510858921883.3
2.2-2.370.0866.710690909181.9
2.37-2.610.0737.810276877979.5
2.61-2.990.0549.911107948785.5
2.99-3.760.0411310072867279.4
3.760.03116.210932935484.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.832 Å / Cor.coef. Fo:Fc: 0.9568 / Cor.coef. Fo:Fc free: 0.9436 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. 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. 3. 1,2 ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT AND FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. ZINC IONS ARE MODELED IN THE STRUCTURE. THE ASSIGNMENT OF ZINC IS SUPPORTED BY COORDINATION GEOMETRY, ANOMALOUS DIFFERENCE FOURIER MAPS AND X-RAY FLUORESCENCE SCANS (WHICH SHOWED A PEAK FOR ZINC). ZINC WAS NOT ADDED DURING CRYSTALLIZATION OR PURIFICATION AND CO-PURIFIED WITH THE PROTEIN. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 6. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2597 5.04 %RANDOM
Rwork0.1478 ---
obs0.1491 51539 92.81 %-
Displacement parametersBiso max: 96.46 Å2 / Biso mean: 18.5614 Å2 / Biso min: 5.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.1389 Å20 Å2-0.0834 Å2
2---3.7032 Å20 Å2
3---3.8421 Å2
Refine analyzeLuzzati coordinate error obs: 0.164 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 66 641 5136
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2192SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes720HARMONIC5
X-RAY DIFFRACTIONt_it4764HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion579SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6035SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4764HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6470HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion4.49
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2113 181 4.62 %
Rwork0.1959 3734 -
all0.1966 3915 -
obs--92.81 %
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)
10.4776-0.01750.15670.4795-0.27920.56830.0152-0.06-0.05150.04820.03530.03590.0126-0.0624-0.0505-0.02770.00330.0131-0.01560.0169-0.0124-3.89716.636573.4464
20.49060.0057-0.00010.3636-0.2580.5333-0.0076-0.01270.0240.0450.0128-0.0039-0.0474-0.0193-0.0052-0.02480.00240.0062-0.0202-0.0003-0.01292.341818.528964.3692
30.24530.0006-0.06240.4163-0.27451.06320.00740.01950.0157-0.03270.0248-0.003-0.0492-0.0481-0.0322-0.0296-0.00460.0047-0.02210.0077-0.01559.5839.559226.9054
40.21430.0675-0.18870.508-0.2870.69520.0073-0.01930.00270.02260.03230.0166-0.0401-0.0845-0.0397-0.0364-0.00080.0002-0.01320.0074-0.00882.905934.823541.0722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|25 - 157}A25 - 157
2X-RAY DIFFRACTION2{A|158 - 304}A158 - 304
3X-RAY DIFFRACTION3{B|26 - 157}B26 - 157
4X-RAY DIFFRACTION4{B|158 - 304}B158 - 304

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