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- PDB-4jph: Crystal structure of Protein Related to DAN and Cerberus (PRDC) -

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Basic information

Entry
Database: PDB / ID: 4jph
TitleCrystal structure of Protein Related to DAN and Cerberus (PRDC)
ComponentsGremlin-2
KeywordsCYTOKINE / Cystine knot / DAN domain / CAN domain / BMP antagonist / BMP-2 / BMP-4 / BMP-7 / GDF-5 / GSH / extracellular
Function / homology
Function and homology information


sequestering of BMP from receptor via BMP binding / regulation of cytokine activity / determination of dorsal identity / Signaling by BMP / embryonic body morphogenesis / BMP binding / negative regulation of BMP signaling pathway / cytokine activity / animal organ morphogenesis / cytokine-mediated signaling pathway ...sequestering of BMP from receptor via BMP binding / regulation of cytokine activity / determination of dorsal identity / Signaling by BMP / embryonic body morphogenesis / BMP binding / negative regulation of BMP signaling pathway / cytokine activity / animal organ morphogenesis / cytokine-mediated signaling pathway / heparin binding / receptor ligand activity / extracellular space / identical protein binding
Similarity search - Function
Gremlin-1/2 / DAN / DAN domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / GLUTATHIONE / Gremlin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsDeng, X. / Nolan, K.T. / Kattamuri, C. / Thompson, T.B.
CitationJournal: Structure / Year: 2013
Title: Structure of protein related to dan and cerberus: insights into the mechanism of bone morphogenetic protein antagonism.
Authors: Nolan, K. / Kattamuri, C. / Luedeke, D.M. / Deng, X. / Jagpal, A. / Zhang, F. / Linhardt, R.J. / Kenny, A.P. / Zorn, A.M. / Thompson, T.B.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gremlin-2
B: Gremlin-2
C: Gremlin-2
D: Gremlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,27322
Polymers68,5554
Non-polymers2,71918
Water2,036113
1
A: Gremlin-2
B: Gremlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,82113
Polymers34,2772
Non-polymers1,54411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-32 kcal/mol
Surface area13560 Å2
MethodPISA
2
C: Gremlin-2
D: Gremlin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4539
Polymers34,2772
Non-polymers1,1757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-28 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.312, 65.558, 85.077
Angle α, β, γ (deg.)90.00, 105.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Gremlin-2 / Cysteine knot superfamily 1 / BMP antagonist 2 / Protein related to DAN and cerberus


Mass: 17138.678 Da / Num. of mol.: 4 / Fragment: UNP residues 22-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Grem2, Cktsf1b2, Prdc / Production host: Escherichia coli (E. coli) / References: UniProt: O88273
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG3350, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9574 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 18, 2011 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9574 Å / Relative weight: 1
ReflectionResolution: 2.25→17.6 Å / Num. all: 36786 / Num. obs: 36786 / % possible obs: 99.27 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 67.13 Å2
Reflection shellHighest resolution: 2.25 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHELXSphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→17.6 Å / Cor.coef. Fo:Fc: 0.9536 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.159 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1838 5 %RANDOM
Rwork0.2023 ---
obs0.2034 36786 99.27 %-
all-36786 --
Displacement parametersBiso mean: 83.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.4353 Å20 Å2-0.8522 Å2
2---3.1576 Å20 Å2
3---0.7223 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.25→17.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 146 113 3730
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013815HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.25193HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1362SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3815HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion18.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion474SEMIHARMONIC5
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_contact3981SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2528 138 4.88 %
Rwork0.2316 2689 -
all0.2327 2827 -
obs--99.27 %
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)
16.71431.9788-1.37720.56240.0037-0.92810.17890.27130.867-0.0343-0.07110.1817-0.0850.0353-0.1077-0.41110.0838-0.0342-0.19970.0536-0.2743-5.433916.903849.3294
25.43763.28971.73812.09330.69361.30290.1867-0.344-0.3327-0.0485-0.1332-0.09470.16020.1247-0.0534-0.37640.1133-0.0552-0.3871-0.054-0.3388-20.11015.629152.717
32.21872.51773.54222.3043.50236.76140.28510.04580.32390.3058-0.09120.18721.0098-0.5131-0.1939-0.2613-0.1148-0.0497-0.42870.0843-0.432311.07425.598919.2788
43.6927-0.29546.49390.80841.28049.84370.3640.16640.0330.3278-0.10890.15270.764-0.0554-0.2551-0.2728-0.249-0.0274-0.16230.1707-0.47673.03280.13430.3326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A46 - 160
2X-RAY DIFFRACTION2{ B|* }B50 - 160
3X-RAY DIFFRACTION3{ C|* }C60 - 160
4X-RAY DIFFRACTION4{ D|* }D50 - 160

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