HEADER HORMONE 21-JUN-12 2LUU TITLE NMR SOLUTION STRUCTURE OF MIDKINE-B, MDKB COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIDKINE-RELATED GROWTH FACTOR MDK2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 22-147; COMPND 5 SYNONYM: UNCHARACTERIZED PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: MDKB, MDK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-4T-1 KEYWDS BETA SHEET, INDEPENDENT HALF-DOMAIN, DISULFIDE BOND, HORMONE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.YANG,J.LIM,D.MENG REVDAT 2 14-JUN-23 2LUU 1 REMARK SEQADV REVDAT 1 01-MAY-13 2LUU 0 JRNL AUTH J.LIM,S.YAO,M.GRAF,C.WINKLER,D.YANG JRNL TITL STRUCTURE-FUNCTION ANALYSIS OF FULL-LENGTH MIDKINE REVEALS JRNL TITL 2 NOVEL RESIDUES IMPORTANT FOR HEPARIN BINDING AND ZEBRAFISH JRNL TITL 3 EMBRYOGENESIS. JRNL REF BIOCHEM.J. V. 451 407 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23418741 JRNL DOI 10.1042/BJ20121622 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOE DISTANCE REFINEMENT USING CYANA REMARK 3 2.1. HYDROGEN BOND RESTRAINTS USING H-D EXCHANGE EXPERIMENT REMARK 4 REMARK 4 2LUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000102861. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10 MM POTASSIUM PHOSPHATE, 0.1 REMARK 210 MM SODIUM AZIDE, 100 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 0.8 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HN(CO)CA; 3D HNCA; 3D MQ-(H) REMARK 210 CCH-TOCSY; 4D TIMESHARED 13C/ REMARK 210 15N EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRSPY, TALOS, NMRPIPE 1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 ASP A 15 177.49 61.26 REMARK 500 1 ALA A 16 44.78 -172.30 REMARK 500 1 GLU A 20 63.30 -112.78 REMARK 500 1 GLN A 22 95.54 -63.02 REMARK 500 1 ASN A 43 -71.55 71.20 REMARK 500 1 GLU A 44 35.10 176.87 REMARK 500 1 PRO A 54 78.22 -69.76 REMARK 500 1 ASP A 60 -75.07 -133.65 REMARK 500 1 ALA A 73 -175.58 54.03 REMARK 500 1 THR A 78 -74.34 -51.68 REMARK 500 1 ALA A 91 -80.23 -89.68 REMARK 500 1 LEU A 92 -168.55 50.57 REMARK 500 1 PHE A 93 106.44 62.05 REMARK 500 1 ASN A 94 -77.81 67.88 REMARK 500 1 ALA A 95 -71.13 -144.45 REMARK 500 1 LYS A 110 -176.39 -172.71 REMARK 500 1 THR A 111 73.25 54.75 REMARK 500 1 PRO A 112 92.56 -69.68 REMARK 500 2 MET A 3 -70.34 -56.49 REMARK 500 2 LYS A 4 84.12 56.37 REMARK 500 2 GLU A 7 179.81 59.32 REMARK 500 2 ASP A 15 175.27 60.82 REMARK 500 2 GLU A 20 66.06 -109.67 REMARK 500 2 GLN A 22 99.32 -64.79 REMARK 500 2 ASN A 43 -70.99 71.49 REMARK 500 2 GLU A 44 35.29 176.66 REMARK 500 2 PRO A 54 78.23 -69.75 REMARK 500 2 ASP A 60 -170.83 -175.51 REMARK 500 2 PHE A 61 -179.06 62.14 REMARK 500 2 ALA A 73 -175.08 -56.49 REMARK 500 2 THR A 78 -75.46 -52.19 REMARK 500 2 ALA A 91 41.78 -151.21 REMARK 500 2 LEU A 92 -169.59 -68.39 REMARK 500 2 ASN A 94 -76.02 69.10 REMARK 500 2 ALA A 95 108.04 -52.40 REMARK 500 2 PRO A 106 98.26 -69.76 REMARK 500 2 THR A 111 70.59 -119.15 REMARK 500 2 PRO A 112 -176.07 -69.75 REMARK 500 2 LYS A 113 73.51 59.99 REMARK 500 2 PRO A 114 -173.19 -69.81 REMARK 500 3 LYS A 4 179.29 57.81 REMARK 500 3 LYS A 13 88.47 -152.00 REMARK 500 3 ASP A 15 172.98 61.00 REMARK 500 3 ALA A 16 58.10 -145.05 REMARK 500 3 GLU A 20 62.98 -114.98 REMARK 500 3 ASP A 32 -54.64 -155.18 REMARK 500 3 GLU A 44 81.59 71.48 REMARK 500 3 GLN A 45 160.50 179.11 REMARK 500 3 PRO A 54 77.74 -69.81 REMARK 500 3 LYS A 58 -70.16 -96.48 REMARK 500 REMARK 500 THIS ENTRY HAS 209 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MKN RELATED DB: PDB REMARK 900 N-HALF DOMAIN REMARK 900 RELATED ID: 1MKC RELATED DB: PDB REMARK 900 C-HALF DOMAIN REMARK 900 RELATED ID: 2LUT RELATED DB: PDB REMARK 900 RELATED ID: 18541 RELATED DB: BMRB DBREF 2LUU A 2 127 UNP Q9DDG2 Q9DDG2_DANRE 22 147 SEQADV 2LUU GLY A 1 UNP Q9DDG2 EXPRESSION TAG SEQRES 1 A 127 GLY SER MET LYS LYS LYS GLU LYS GLY LYS GLU PRO LYS SEQRES 2 A 127 ALA ASP ALA GLU CYS SER GLU TRP GLN TYR GLY LYS CYS SEQRES 3 A 127 VAL PRO ASN SER GLY ASP CYS GLY ASN GLY ILE ARG GLU SEQRES 4 A 127 ALA THR CYS ASN GLU GLN THR LYS LYS THR LYS CYS LYS SEQRES 5 A 127 VAL PRO CYS ASN TRP LYS LYS ASP PHE GLY ALA ASP CYS SEQRES 6 A 127 LYS TYR LYS PHE GLY ARG TRP ALA GLU CYS ASP THR THR SEQRES 7 A 127 THR GLY THR ARG SER ARG SER GLY THR LEU LYS LYS ALA SEQRES 8 A 127 LEU PHE ASN ALA GLU CYS GLN THR THR ILE LYS VAL SER SEQRES 9 A 127 LYS PRO CYS THR PRO LYS THR PRO LYS PRO LYS GLY GLY SEQRES 10 A 127 GLU LYS LYS LYS GLY LYS GLY LYS GLU ASN SHEET 1 A 3 VAL A 27 PRO A 28 0 SHEET 2 A 3 ASN A 35 CYS A 42 -1 O ILE A 37 N VAL A 27 SHEET 3 A 3 GLN A 45 LYS A 52 -1 O CYS A 51 N GLY A 36 SHEET 1 B 3 LYS A 66 LYS A 68 0 SHEET 2 B 3 THR A 81 LYS A 90 -1 O LYS A 90 N LYS A 66 SHEET 3 B 3 ILE A 101 PRO A 106 -1 O LYS A 105 N ARG A 82 SSBOND 1 CYS A 18 CYS A 42 1555 1555 2.00 SSBOND 2 CYS A 26 CYS A 51 1555 1555 2.00 SSBOND 3 CYS A 33 CYS A 55 1555 1555 1.99 SSBOND 4 CYS A 65 CYS A 97 1555 1555 1.98 SSBOND 5 CYS A 75 CYS A 107 1555 1555 2.11 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