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- PDB-3dmb: Crystal structure of a putative general stress family protein (xc... -

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Entry
Database: PDB / ID: 3dmb
TitleCrystal structure of a putative general stress family protein (xcc2264) from xanthomonas campestris pv. campestris at 2.30 A resolution
ComponentsPutative General Stress Protein 26 with a PNP-Oxidase like Fold
KeywordsOXIDOREDUCTASE / Pnp-oxidase like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyGeneral stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / General stress protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative General Stress Protein 26 with a PNP-Oxidase like Fold (NP_637619.1) from XANTHOMONAS CAMPESTRIS at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 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 / Derived calculations / Refinement description
Category: software / struct_conn
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
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
B: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
C: Putative General Stress Protein 26 with a PNP-Oxidase like Fold


Theoretical massNumber of molelcules
Total (without water)48,4313
Polymers48,4313
Non-polymers00
Water1,15364
1
A: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
B: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
C: Putative General Stress Protein 26 with a PNP-Oxidase like Fold

A: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
B: Putative General Stress Protein 26 with a PNP-Oxidase like Fold
C: Putative General Stress Protein 26 with a PNP-Oxidase like Fold


Theoretical massNumber of molelcules
Total (without water)96,8626
Polymers96,8626
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area17400 Å2
ΔGint-129 kcal/mol
Surface area37490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.320, 105.320, 68.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-167-

HOH

21C-160-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 255 - 25
21BB5 - 255 - 25
31CC5 - 255 - 25
42AA34 - 13234 - 132
52BB34 - 13234 - 132
62CC34 - 13234 - 132
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A HEXAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative General Stress Protein 26 with a PNP-Oxidase like Fold


Mass: 16143.693 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: NP_637619.1, XCC2264 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8P8H7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT CONTAINS AMINO ACIDS 1-146 OF THE FULL LENGTH PROTEIN OF 162 RESIDUES. THE CONSTRUCT ...THE CONSTRUCT CONTAINS AMINO ACIDS 1-146 OF THE FULL LENGTH PROTEIN OF 162 RESIDUES. 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.2000M K2HPO4, 0.8000M Na2HPO4, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97862,0.91837,0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 16, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978621
20.918371
30.979391
ReflectionResolution: 2.3→28.665 Å / Num. obs: 19745 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.88 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.380.6422.113091354596
2.38-2.480.4962.814906391599.7
2.48-2.590.3773.814154370299.9
2.59-2.730.294.814776385899.8
2.73-2.90.1777.714203371899.8
2.9-3.120.10212.514413374899.7
3.12-3.430.0619.714357373899.9
3.43-3.930.03530.114711382599.9
3.93-4.930.02343.214440373999.9
4.930.02148.114717382799.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→28.665 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 18.407 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.26
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1006 5.1 %RANDOM
Rwork0.21 ---
obs0.213 19719 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20.54 Å20 Å2
2--1.08 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 0 64 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223316
X-RAY DIFFRACTIONr_bond_other_d0.0030.022241
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9574496
X-RAY DIFFRACTIONr_angle_other_deg1.28135460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7495429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75424.161137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2071518
X-RAY DIFFRACTIONr_chiral_restr0.0960.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023733
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02670
X-RAY DIFFRACTIONr_nbd_refined0.1620.2528
X-RAY DIFFRACTIONr_nbd_other0.1380.21991
X-RAY DIFFRACTIONr_nbtor_refined0.150.21530
X-RAY DIFFRACTIONr_nbtor_other0.070.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1240.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.214
X-RAY DIFFRACTIONr_mcbond_it1.12522402
X-RAY DIFFRACTIONr_mcbond_other0.2352883
X-RAY DIFFRACTIONr_mcangle_it1.76343328
X-RAY DIFFRACTIONr_scbond_it3.07361391
X-RAY DIFFRACTIONr_scangle_it4.4481164
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A694MEDIUM POSITIONAL0.350.5
2B694MEDIUM POSITIONAL0.330.5
3C694MEDIUM POSITIONAL0.280.5
1A807LOOSE POSITIONAL0.835
2B807LOOSE POSITIONAL0.665
3C807LOOSE POSITIONAL0.675
1A694MEDIUM THERMAL0.792
2B694MEDIUM THERMAL0.742
3C694MEDIUM THERMAL0.712
1A807LOOSE THERMAL2.1810
2B807LOOSE THERMAL1.8210
3C807LOOSE THERMAL1.8410
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 74 -
Rwork0.281 1353 -
all-1427 -
obs--98.55 %
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)
18.24691.47221.01810.97830.30353.42730.02240.2345-0.208-0.06590.00910.03630.2098-0.105-0.0314-0.19110.0192-0.0078-0.2845-0.0069-0.29736.83822.91915.748
23.17480.08791.89210.9104-0.4454.7071-0.03380.2244-0.0845-0.0736-0.0107-0.23360.14960.88170.0445-0.17050.05760.058-0.07560.0295-0.158927.24121.26916.909
30.31140.8513-0.0893.05892.29638.83360.3686-0.02920.13180.3207-0.36480.0896-1.8754-0.0964-0.00370.4092-0.20070.0293-0.2317-0.0078-0.086423.35752.439.367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1451 - 146
2X-RAY DIFFRACTION2BB1 - 1452 - 146
3X-RAY DIFFRACTION3CC4 - 245 - 25
4X-RAY DIFFRACTION3CC33 - 14534 - 146

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