PDB Short entry for 2KDB HEADER PROTEIN BINDING 06-JAN-09 2KDB TITLE SOLUTION STRUCTURE OF HUMAN UBIQUITIN-LIKE DOMAIN OF HERPUD2_9_85, TITLE 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET HT53A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT COMPND 3 UBIQUITIN-LIKE DOMAIN MEMBER 2 PROTEIN; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UBIQUITIN-LIKE DOMAIN, RESIDUES 9-85; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HERPUD2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS UBL DOMAIN, MEMBRANE, TRANSMEMBRANE, UNFOLDED PROTEIN RESPONSE, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, NESG, ONTARIO CENTRE FOR STRUCTURAL KEYWDS 4 PROTEOMICS, OCSP, UNKNOWN FUNCTION, PROTEIN BINDING, SGC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.WU,A.YEE,C.FARES,A.LEMAK,A.GUTMANAS,R.DOHERTY,A.SEMESI,S.DHE- AUTHOR 2 PAGANON,C.ARROWSMITH,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (NESG),STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 23-MAY-12 2KDB 1 REMARK VERSN REVDAT 2 02-JUN-09 2KDB 1 JRNL REVDAT 1 10-FEB-09 2KDB 0 JRNL AUTH R.DOHERTY,B.WU,C.FARES,A.LEMAK,A.GUTMANAS,A.SEMESI,A.YEE, JRNL AUTH 2 C.H.ARROWSMITH,S.DHE-PAGANON JRNL TITL STRUCTURE OF HUMAN HOMOCYSTEINE-INDUCIBLE, ENDOPLASMIC JRNL TITL 2 RETICULUM STRESS-INDUCIBLE, UBIQUITIN-LIKE DOMAIN MEMBER 2 JRNL TITL 3 (HERPUD2 OR HERP) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LEMAK,A.GUTMANAS,S.CHITAYAT,M.KARRA,C.FARES,M.SUNNERHAGEN, REMARK 1 AUTH 2 C.H.ARROWSMITH REMARK 1 TITL A NOVEL STRATEGY FOR NMR RESONANCE ASSIGNMENT AND PROTEIN REMARK 1 TITL 2 STRUCTURE DETERMINATION. REMARK 1 REF J.BIOMOL.NMR V. 49 27 2011 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 21161328 REMARK 1 DOI 10.1007/S10858-010-9458-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-09. REMARK 100 THE RCSB ID CODE IS RCSB100978. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 300; 300; 300 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 HUMNA UBIQUITIN-LIKE DOMAIN OF REMARK 210 HERP-1, 10 MM [U-100% 2H] TRIS-2, REMARK 210 300 MM SODIUM CHLORIDE-3, 0.01 % REMARK 210 SODIUM AZIDE-4, 10 MM BENZAMIDINE REMARK 210 -5, 90% H2O/10% D2O; 0.5 MM [U- REMARK 210 100% 13C; U-100% 15N] HUMNA REMARK 210 UBIQUITIN-LIKE DOMAIN OF HERP-6, REMARK 210 10 MM [U-100% 2H] TRIS-7, 300 MM REMARK 210 SODIUM CHLORIDE-8, 0.01 % SODIUM REMARK 210 AZIDE-9, 10 MM BENZAMIDINE-10, REMARK 210 100% D2O; 0.5 MM [U-7% 13C; U- REMARK 210 100% 15N] HUMNA UBIQUITIN-LIKE REMARK 210 DOMAIN OF HERP-11, 10 MM [U-100% REMARK 210 2H] TRIS-12, 300 MM SODIUM REMARK 210 CHLORIDE-13, 0.01 % SODIUM AZIDE- REMARK 210 14, 10 MM BENZAMIDINE-15, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HNCA; 3D HCCH- REMARK 210 TOCSY; 3D CCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MNRPIPE 2.3, SPARKY 3.95, FAWN REMARK 210 1.0, CYANA 2.1, AUTOSTRUCTURE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 ARG A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 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 SER A 14 -177.26 -68.81 REMARK 500 1 ASP A 69 -55.61 70.73 REMARK 500 2 ASP A 15 102.47 -57.83 REMARK 500 2 SER A 51 18.62 56.25 REMARK 500 2 ASP A 69 -55.84 73.49 REMARK 500 3 ASP A 15 100.25 -58.74 REMARK 500 3 LYS A 40 78.16 56.08 REMARK 500 3 ASP A 69 -47.51 75.49 REMARK 500 4 GLN A 11 -48.63 80.31 REMARK 500 4 LYS A 40 65.57 60.84 REMARK 500 4 PRO A 41 100.07 -48.24 REMARK 500 4 ASP A 45 -60.57 -125.65 REMARK 500 4 ASP A 69 18.68 57.49 REMARK 500 4 GLU A 70 -63.90 -136.03 REMARK 500 5 SER A 14 -157.88 -81.53 REMARK 500 5 LYS A 40 73.13 51.31 REMARK 500 5 ASP A 69 -67.25 67.31 REMARK 500 6 LYS A 40 76.94 56.23 REMARK 500 6 ASP A 69 -24.45 71.21 REMARK 500 6 GLU A 70 -60.21 -92.16 REMARK 500 7 ASN A 10 -72.01 -111.96 REMARK 500 7 GLN A 11 36.14 -170.44 REMARK 500 7 SER A 14 -162.51 -76.26 REMARK 500 7 ASP A 69 -78.96 63.40 REMARK 500 8 ASP A 15 85.65 -69.50 REMARK 500 8 ASP A 69 -64.39 69.49 REMARK 500 9 ASP A 15 95.91 -61.83 REMARK 500 9 ASP A 69 104.96 -27.19 REMARK 500 9 GLU A 70 -65.55 -164.98 REMARK 500 10 LYS A 40 79.42 54.66 REMARK 500 10 ASP A 69 -59.28 72.13 REMARK 500 11 LYS A 40 72.24 58.18 REMARK 500 11 ASP A 69 -47.49 74.80 REMARK 500 11 GLU A 70 -93.61 -77.15 REMARK 500 12 GLN A 11 88.97 -39.84 REMARK 500 12 ASP A 15 86.81 -56.47 REMARK 500 12 LYS A 40 82.00 53.19 REMARK 500 12 SER A 51 -2.45 65.72 REMARK 500 12 ASP A 69 -50.87 73.58 REMARK 500 12 GLU A 70 -93.91 -70.38 REMARK 500 13 ASP A 15 93.41 -68.10 REMARK 500 13 LYS A 40 73.02 55.91 REMARK 500 13 SER A 51 -0.82 64.11 REMARK 500 14 LYS A 40 74.54 52.58 REMARK 500 14 ASP A 69 -62.35 72.56 REMARK 500 14 GLU A 70 -78.29 -78.55 REMARK 500 15 ASN A 10 -78.90 -121.15 REMARK 500 15 GLN A 11 55.78 -163.75 REMARK 500 15 ASP A 15 86.87 -65.25 REMARK 500 15 ASP A 69 -65.67 69.69 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HT53A RELATED DB: TARGETDB DBREF 2KDB A 1 77 UNP Q9BSE4 HERP2_HUMAN 9 85 SEQADV 2KDB MET A -21 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB GLY A -20 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB SER A -19 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB SER A -18 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -17 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -16 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -15 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -14 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -13 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A -12 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB SER A -11 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB SER A -10 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB GLY A -9 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB ARG A -8 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB GLU A -7 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB ASN A -6 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB LEU A -5 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB TYR A -4 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB PHE A -3 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB GLN A -2 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB GLY A -1 UNP Q9BSE4 EXPRESSION TAG SEQADV 2KDB HIS A 0 UNP Q9BSE4 EXPRESSION TAG SEQRES 1 A 99 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 99 ARG GLU ASN LEU TYR PHE GLN GLY HIS PRO VAL THR LEU SEQRES 3 A 99 ILE ILE LYS ALA PRO ASN GLN LYS TYR SER ASP GLN THR SEQRES 4 A 99 ILE SER CYS PHE LEU ASN TRP THR VAL GLY LYS LEU LYS SEQRES 5 A 99 THR HIS LEU SER ASN VAL TYR PRO SER LYS PRO LEU THR SEQRES 6 A 99 LYS ASP GLN ARG LEU VAL TYR SER GLY ARG LEU LEU PRO SEQRES 7 A 99 ASP HIS LEU GLN LEU LYS ASP ILE LEU ARG LYS GLN ASP SEQRES 8 A 99 GLU TYR HIS MET VAL HIS LEU VAL HELIX 1 1 THR A 25 TYR A 37 1 13 HELIX 2 2 LEU A 61 ARG A 66 1 6 SHEET 1 A 5 GLN A 16 CYS A 20 0 SHEET 2 A 5 VAL A 2 LYS A 7 -1 N ILE A 6 O GLN A 16 SHEET 3 A 5 TYR A 71 LEU A 76 1 O LEU A 76 N LYS A 7 SHEET 4 A 5 LEU A 48 TYR A 50 -1 N VAL A 49 O HIS A 75 SHEET 5 A 5 ARG A 53 LEU A 55 -1 O LEU A 55 N LEU A 48 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