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- PDB-3jyg: Crystal structure of uncharacterized protein WS1659 from Wolinell... -

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Basic information

Entry
Database: PDB / ID: 3jyg
TitleCrystal structure of uncharacterized protein WS1659 from Wolinella succinogenes
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


6-carboxytetrahydropterin synthase / 6-carboxy-5,6,7,8-tetrahydropterin synthase activity / metal ion binding
Similarity search - Function
6-pyruvoyl tetrahydropterin synthase/QueD / 6-pyruvoyl tetrahydropterin synthase/QueD family / 6-pyruvoyl tetrahydropterin synthase/QueD superfamily / 6-pyruvoyl tetrahydropterin synthase / Tetrahydropterin Synthase; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-carboxy-5,6,7,8-tetrahydropterin synthase
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein WS1659 from Wolinella succinogenes
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,98812
Polymers133,5966
Non-polymers3926
Water12,647702
1
A: Uncharacterized protein
B: Uncharacterized protein
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9946
Polymers66,7983
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-135 kcal/mol
Surface area24050 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9946
Polymers66,7983
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-137 kcal/mol
Surface area23920 Å2
MethodPISA
3
A: Uncharacterized protein
B: Uncharacterized protein
E: Uncharacterized protein
hetero molecules

C: Uncharacterized protein
D: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,98812
Polymers133,5966
Non-polymers3926
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area22840 Å2
ΔGint-362 kcal/mol
Surface area39990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.838, 80.949, 104.614
Angle α, β, γ (deg.)90.000, 113.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 22265.943 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: WS1659 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MR56
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% Jeffamine ED-2001 pH 7.0, 1.1M Sodium Malonate pH 7.0, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 106182 / Num. obs: 106182 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.112 / Rsym value: 0.088 / Χ2: 1.081 / Net I/σ(I): 7.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.9 / Num. unique all: 19589 / Rsym value: 0.399 / Χ2: 0.816 / % possible all: 93.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
SOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.852 / SU B: 3.494 / SU ML: 0.102 / SU R Cruickshank DPI: 0.152 / SU Rfree: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5293 5 %RANDOM
Rwork0.192 ---
obs0.194 106161 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.4 Å2 / Biso mean: 21.685 Å2 / Biso min: 3.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.06 Å2
2---0.78 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9002 0 6 702 9710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229265
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.94812573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17951096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09722.727473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.335151586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0271582
X-RAY DIFFRACTIONr_chiral_restr0.1150.21355
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217124
X-RAY DIFFRACTIONr_mcbond_it0.9781.55439
X-RAY DIFFRACTIONr_mcangle_it1.78228862
X-RAY DIFFRACTIONr_scbond_it2.8633826
X-RAY DIFFRACTIONr_scangle_it4.4054.53700
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 337 -
Rwork0.23 6375 -
all-6712 -
obs--84.75 %

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