HEADER UNKNOWN FUNCTION 07-MAR-19 6O6W TITLE SOLUTION STRUCTURE OF HUMAN MYELOID-DERIVED GROWTH FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID-DERIVED GROWTH FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MYDGF; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CLONING RESIDUES: G1-T5 MATURE HUMAN MYDGF: V6-L147 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: HUMAN BLOOD EOSINOPHILS; SOURCE 6 GENE: MYDGF, C19ORF10; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: MILLIPORESIGMA 71400; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET-ELMER KEYWDS ENDOPLASMIC RETICULUM, UPF0556, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR V.BORTNOV,M.TONELLI,W.LEE,J.L.MARKLEY,D.F.MOSHER REVDAT 6 20-NOV-24 6O6W 1 REMARK REVDAT 5 14-JUN-23 6O6W 1 REMARK REVDAT 4 15-JUL-20 6O6W 1 SOURCE REMARK HELIX SHEET REVDAT 4 2 1 SSBOND ATOM REVDAT 3 25-DEC-19 6O6W 1 JRNL REVDAT 2 18-DEC-19 6O6W 1 REMARK REVDAT 1 13-NOV-19 6O6W 0 JRNL AUTH V.BORTNOV,M.TONELLI,W.LEE,Z.LIN,D.S.ANNIS,O.N.DEMERDASH, JRNL AUTH 2 A.BATEMAN,J.C.MITCHELL,Y.GE,J.L.MARKLEY,D.F.MOSHER JRNL TITL SOLUTION STRUCTURE OF HUMAN MYELOID-DERIVED GROWTH FACTOR JRNL TITL 2 SUGGESTS A CONSERVED FUNCTION IN THE ENDOPLASMIC RETICULUM. JRNL REF NAT COMMUN V. 10 5612 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31819058 JRNL DOI 10.1038/S41467-019-13577-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PYMOL, PONDEROSA-C/S, X-PLOR NIH REMARK 3 AUTHORS : SCHROEDINGER, INC. (PYMOL), W. LEE, J.L. STARK, REMARK 3 J.L. MARKLEY (PONDEROSA-C/S), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EXPLICIT WATER REFINEMENT REMARK 4 REMARK 4 6O6W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000239248. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 135 (NACL) REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 8.25 MG/ML U-15N; U-13C; NA-H REMARK 210 MYDGF, 9 MM NA SODIUM PHOSPHATE, REMARK 210 135 MM NA SODIUM CHLORIDE, 15 UM REMARK 210 NA DSS, 0.02 % W/V NA SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H,15N-HSQC NOESY; 3D 1H,13C REMARK 210 -HSQC NOESY ALIPHATIC; 3D 1H,13C- REMARK 210 HSQC NOESY AROMATIC; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 2D 1H-13C HSQC AROMATIC; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCO; REMARK 210 3D C(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY ALIPHATIC; 3D H(CCO) REMARK 210 NH; 2D (HB)CB(CGCD)HD AROMATIC; REMARK 210 2D (HB)CB(CGCDCE)HDHE AROMATIC; REMARK 210 3D HCCH-TOCSY AROMATIC; 3D 1H, REMARK 210 15N-HSQC NOESY 1H,13C-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : VNS; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 4.2, TOPSPIN 3.5, NMRPIPE, REMARK 210 NMRFAM-SPARKY, I-PINE, PONDEROSA- REMARK 210 C/S, TALOS-N, X-PLOR NIH REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 THR A 5 97.85 49.90 REMARK 500 1 GLU A 103 -107.59 50.07 REMARK 500 2 GLU A 103 -108.76 58.21 REMARK 500 2 SER A 134 -55.63 -129.98 REMARK 500 2 ARG A 144 -176.36 49.26 REMARK 500 2 THR A 145 85.73 53.60 REMARK 500 3 GLU A 103 -109.35 56.96 REMARK 500 4 LYS A 3 -68.75 71.45 REMARK 500 4 GLU A 103 -109.16 51.21 REMARK 500 4 SER A 134 -69.13 -127.99 REMARK 500 4 THR A 145 100.04 58.64 REMARK 500 5 GLU A 103 -109.52 55.97 REMARK 500 5 ALA A 131 32.70 71.28 REMARK 500 5 SER A 134 -54.35 -140.25 REMARK 500 6 THR A 5 100.27 55.14 REMARK 500 6 SER A 7 34.29 -95.10 REMARK 500 6 GLU A 103 -108.12 52.09 REMARK 500 6 SER A 134 -50.46 -135.21 REMARK 500 6 GLU A 146 156.01 65.58 REMARK 500 7 SER A 7 82.64 -162.82 REMARK 500 7 GLU A 103 -108.91 56.34 REMARK 500 7 ALA A 131 30.38 72.41 REMARK 500 7 SER A 134 -54.68 -133.70 REMARK 500 7 SER A 143 -176.57 49.98 REMARK 500 7 THR A 145 88.37 56.84 REMARK 500 8 SER A 7 -31.08 -167.59 REMARK 500 8 GLU A 103 -108.93 54.63 REMARK 500 9 SER A 2 177.84 54.36 REMARK 500 9 LYS A 3 125.19 62.92 REMARK 500 9 TYR A 76 57.25 -108.07 REMARK 500 9 GLU A 103 -108.17 54.47 REMARK 500 9 ALA A 128 -53.97 -122.52 REMARK 500 10 LYS A 3 -78.48 65.29 REMARK 500 10 GLU A 103 -108.52 55.27 REMARK 500 10 THR A 120 21.96 -150.87 REMARK 500 10 ALA A 131 37.95 72.16 REMARK 500 10 SER A 134 -46.35 -133.27 REMARK 500 10 ARG A 144 -47.28 72.77 REMARK 500 10 THR A 145 94.17 47.96 REMARK 500 11 THR A 5 147.03 58.81 REMARK 500 11 GLU A 103 -107.77 50.17 REMARK 500 11 SER A 134 -34.59 -135.56 REMARK 500 11 SER A 143 -171.70 52.36 REMARK 500 12 GLU A 103 -108.39 55.87 REMARK 500 12 LYS A 130 -85.06 -91.47 REMARK 500 12 ALA A 131 -14.30 -159.75 REMARK 500 12 SER A 134 -44.07 -132.98 REMARK 500 12 THR A 145 -49.04 72.29 REMARK 500 12 GLU A 146 90.57 60.81 REMARK 500 13 SER A 2 -70.56 67.14 REMARK 500 REMARK 500 THIS ENTRY HAS 75 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30584 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF HUMAN MYELOID-DERIVED GROWTH FACTOR DBREF 6O6W A 6 147 UNP Q969H8 MYDGF_HUMAN 32 173 SEQADV 6O6W GLY A 1 UNP Q969H8 EXPRESSION TAG SEQADV 6O6W SER A 2 UNP Q969H8 EXPRESSION TAG SEQADV 6O6W LYS A 3 UNP Q969H8 EXPRESSION TAG SEQADV 6O6W GLY A 4 UNP Q969H8 EXPRESSION TAG SEQADV 6O6W THR A 5 UNP Q969H8 EXPRESSION TAG SEQRES 1 A 147 GLY SER LYS GLY THR VAL SER GLU PRO THR THR VAL ALA SEQRES 2 A 147 PHE ASP VAL ARG PRO GLY GLY VAL VAL HIS SER PHE SER SEQRES 3 A 147 HIS ASN VAL GLY PRO GLY ASP LYS TYR THR CYS MET PHE SEQRES 4 A 147 THR TYR ALA SER GLN GLY GLY THR ASN GLU GLN TRP GLN SEQRES 5 A 147 MET SER LEU GLY THR SER GLU ASP HIS GLN HIS PHE THR SEQRES 6 A 147 CYS THR ILE TRP ARG PRO GLN GLY LYS SER TYR LEU TYR SEQRES 7 A 147 PHE THR GLN PHE LYS ALA GLU VAL ARG GLY ALA GLU ILE SEQRES 8 A 147 GLU TYR ALA MET ALA TYR SER LYS ALA ALA PHE GLU ARG SEQRES 9 A 147 GLU SER ASP VAL PRO LEU LYS THR GLU GLU PHE GLU VAL SEQRES 10 A 147 THR LYS THR ALA VAL ALA HIS ARG PRO GLY ALA PHE LYS SEQRES 11 A 147 ALA GLU LEU SER LYS LEU VAL ILE VAL ALA LYS ALA SER SEQRES 12 A 147 ARG THR GLU LEU HELIX 1 AA1 GLY A 30 LYS A 34 5 5 HELIX 2 AA2 LYS A 111 GLU A 113 5 3 SHEET 1 AA1 6 THR A 10 VAL A 16 0 SHEET 2 AA1 6 GLU A 49 THR A 57 -1 O GLU A 49 N VAL A 16 SHEET 3 AA1 6 HIS A 63 TRP A 69 -1 O THR A 67 N SER A 54 SHEET 4 AA1 6 LYS A 135 ALA A 142 -1 O LEU A 136 N ILE A 68 SHEET 5 AA1 6 ALA A 89 LYS A 99 -1 N TYR A 93 O VAL A 139 SHEET 6 AA1 6 VAL A 108 PRO A 109 -1 O VAL A 108 N LYS A 99 SHEET 1 AA2 5 VAL A 22 VAL A 29 0 SHEET 2 AA2 5 TYR A 35 GLN A 44 -1 O PHE A 39 N PHE A 25 SHEET 3 AA2 5 TYR A 78 ARG A 87 -1 O GLN A 81 N ALA A 42 SHEET 4 AA2 5 ALA A 121 HIS A 124 -1 O VAL A 122 N ALA A 84 SHEET 5 AA2 5 PHE A 115 VAL A 117 -1 N GLU A 116 O ALA A 123 SSBOND 1 CYS A 37 CYS A 66 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1