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- PDB-2hhz: Crystal structure of a pyridoxamine 5'-phosphate oxidase-related ... -

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Basic information

Entry
Database: PDB / ID: 2hhz
TitleCrystal structure of a pyridoxamine 5'-phosphate oxidase-related protein (ssuidraft_2804) from streptococcus suis 89/1591 at 2.00 A resolution
ComponentsPyridoxamine 5'-phosphate oxidase-related
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyElectron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Roll / Mainly Beta / ACETATE ION / PHOSPHATE ION / :
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Pyridoxamine 5'-phosphate oxidase-related (ZP_00875725.1) from STREPTOCOCCUS SUIS 89-1591 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6754
Polymers17,4851
Non-polymers1893
Water1,13563
1
A: Pyridoxamine 5'-phosphate oxidase-related
hetero molecules

A: Pyridoxamine 5'-phosphate oxidase-related
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3508
Polymers34,9712
Non-polymers3796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2650 Å2
ΔGint-50 kcal/mol
Surface area13520 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.000, 71.000, 58.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-162-

HOH

21A-169-

HOH

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-related


Mass: 17485.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 89/1591 / Gene: ZP_00875725.1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2ZZ07, pyridoxal 5'-phosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 40.0% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97934, 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979341
30.979151
ReflectionResolution: 2→29.198 Å / Num. obs: 10580 / % possible obs: 94.4 % / Biso Wilson estimate: 40.243 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.48
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2-2.070.7261.957501548181.4
2.07-2.150.582.665891741191.3
2.15-2.250.4972.968851816191.6
2.25-2.370.3893.870681852194.1
2.37-2.520.314.871351856195.2
2.52-2.710.2585.569591812195.3
2.71-2.990.1518.574221922197.1
2.99-3.420.08812.774461919198.8
3.42-29.1980.052072421910199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXEmodel building
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.198 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.134 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.161
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RESIDUES 107-111 AND 140-144 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. CL, ACT, PO4 MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THERE ARE UNMODELED DENSITY NEAR RESIDUES A122 AND A133. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 503 4.8 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.19276 10536 99.5 %-
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: 42.918 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.21 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2→29.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 10 63 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211145
X-RAY DIFFRACTIONr_bond_other_d0.0020.02733
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9281553
X-RAY DIFFRACTIONr_angle_other_deg0.88131781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75923.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11515179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.648155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_nbd_refined0.1980.2204
X-RAY DIFFRACTIONr_nbd_other0.2060.2715
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2549
X-RAY DIFFRACTIONr_nbtor_other0.0890.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.247
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3810.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.27
X-RAY DIFFRACTIONr_mcbond_it2.3613755
X-RAY DIFFRACTIONr_mcbond_other0.5093285
X-RAY DIFFRACTIONr_mcangle_it3.44951118
X-RAY DIFFRACTIONr_scbond_it5.4918492
X-RAY DIFFRACTIONr_scangle_it6.70211433
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 37 -
Rwork0.286 685 -
obs-722 95.5 %
Refinement TLS params.Method: refined / Origin x: 19.2351 Å / Origin y: 35.9856 Å / Origin z: 25.6993 Å
111213212223313233
T-0.1453 Å2-0.0025 Å2-0.002 Å2--0.0929 Å20.065 Å2---0.1219 Å2
L2.793 °2-0.2817 °20.37 °2-3.9676 °20.0505 °2--1.942 °2
S-0.1713 Å °-0.1685 Å °0.002 Å °-0.0192 Å °0.1445 Å °0.6643 Å °-0.0759 Å °-0.423 Å °0.0268 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDAuth seq-IDLabel seq-ID
11 - 1062 - 107
2112 - 139113 - 140
3145 - 149146 - 150

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