PDB Short entry for 5K57 HEADER HYDROLASE 23-MAY-16 5K57 TITLE HDD DOMAIN FROM HUMAN DDI2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DDI1 HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 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: DDI2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DDI2, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR V.VEVERKA REVDAT 3 14-JUN-23 5K57 1 REMARK REVDAT 2 08-MAY-19 5K57 1 REMARK REVDAT 1 10-AUG-16 5K57 0 JRNL AUTH M.SIVA,M.SVOBODA,V.VEVERKA,J.F.TREMPE,K.HOFMANN,M.KOZISEK, JRNL AUTH 2 R.HEXNEROVA,F.SEDLAK,J.BELZA,J.BRYNDA,P.SACHA,M.HUBALEK, JRNL AUTH 3 J.STARKOVA,I.FLAISIGOVA,J.KONVALINKA,K.G.SASKOVA JRNL TITL HUMAN DNA-DAMAGE-INDUCIBLE 2 PROTEIN IS STRUCTURALLY AND JRNL TITL 2 FUNCTIONALLY DISTINCT FROM ITS YEAST ORTHOLOG. JRNL REF SCI REP V. 6 30443 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27461074 JRNL DOI 10.1038/SREP30443 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : HOEGENAUER, KORAIMANN, KUNGL, VRIEND REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5K57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221787. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 280 UM [U-13C; U-15N] HDD, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 SER A 1 CB SER A 1 OG -0.083 REMARK 500 5 SER A 1 CB SER A 1 OG -0.083 REMARK 500 9 SER A 1 CB SER A 1 OG -0.078 REMARK 500 21 SER A 1 CB SER A 1 OG -0.082 REMARK 500 26 SER A 1 CB SER A 1 OG -0.079 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 10 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 22 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 23 ARG A 97 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 27 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 28 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 10 30.09 -88.45 REMARK 500 1 ASP A 53 109.89 -58.43 REMARK 500 1 SER A 80 95.19 -167.03 REMARK 500 1 ALA A 81 31.44 -158.92 REMARK 500 1 ALA A 88 56.10 29.75 REMARK 500 1 ILE A 96 33.31 -91.12 REMARK 500 2 GLU A 10 31.79 -74.44 REMARK 500 2 LEU A 78 -176.54 54.41 REMARK 500 2 PHE A 79 -19.65 61.64 REMARK 500 2 SER A 80 27.61 -152.62 REMARK 500 2 ALA A 81 18.99 -141.15 REMARK 500 2 ALA A 88 30.56 -88.31 REMARK 500 2 ALA A 90 174.78 67.11 REMARK 500 2 LYS A 91 156.52 66.95 REMARK 500 3 GLN A 2 44.34 -152.19 REMARK 500 3 GLN A 3 -150.99 60.41 REMARK 500 3 SER A 14 63.54 -150.78 REMARK 500 3 GLN A 16 28.15 -76.73 REMARK 500 3 LEU A 78 -46.60 -140.38 REMARK 500 3 ALA A 81 42.07 -148.54 REMARK 500 4 SER A 13 -162.46 -162.28 REMARK 500 4 SER A 14 62.47 -112.90 REMARK 500 4 ASP A 53 102.07 -55.21 REMARK 500 4 LEU A 78 -52.76 65.94 REMARK 500 4 ARG A 97 27.15 49.22 REMARK 500 5 GLN A 3 -56.61 -168.05 REMARK 500 5 SER A 4 176.66 64.00 REMARK 500 5 SER A 14 70.38 -115.55 REMARK 500 5 ASP A 53 104.60 -55.81 REMARK 500 5 PHE A 79 -145.96 54.74 REMARK 500 5 ALA A 81 37.33 -98.22 REMARK 500 5 ASP A 85 43.42 -93.59 REMARK 500 5 ALA A 88 38.57 -77.77 REMARK 500 5 ASP A 95 48.58 -151.73 REMARK 500 6 SER A 14 56.33 -117.35 REMARK 500 6 GLN A 16 36.79 -81.46 REMARK 500 6 LEU A 78 128.61 67.53 REMARK 500 6 ALA A 81 36.00 -151.55 REMARK 500 6 ASP A 85 40.84 -84.31 REMARK 500 6 ALA A 88 45.13 -78.22 REMARK 500 6 ARG A 97 42.46 -83.90 REMARK 500 7 ILE A 11 5.86 -68.56 REMARK 500 7 ALA A 81 40.23 -84.11 REMARK 500 7 ASP A 85 103.41 63.48 REMARK 500 7 LYS A 91 179.03 66.83 REMARK 500 7 ASP A 95 45.03 -82.22 REMARK 500 7 ARG A 97 43.41 -71.76 REMARK 500 8 GLN A 3 -155.77 56.72 REMARK 500 8 SER A 6 -167.33 63.22 REMARK 500 8 LEU A 78 -121.22 -96.20 REMARK 500 REMARK 500 THIS ENTRY HAS 231 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30097 RELATED DB: BMRB DBREF 5K57 A 2 98 UNP Q5TDH0 DDI2_HUMAN 116 212 SEQADV 5K57 SER A 1 UNP Q5TDH0 EXPRESSION TAG SEQRES 1 A 98 SER GLN GLN SER HIS SER SER PRO GLY GLU ILE THR SER SEQRES 2 A 98 SER PRO GLN GLY LEU ASP ASN PRO ALA LEU LEU ARG ASP SEQRES 3 A 98 MET LEU LEU ALA ASN PRO HIS GLU LEU SER LEU LEU LYS SEQRES 4 A 98 GLU ARG ASN PRO PRO LEU ALA GLU ALA LEU LEU SER GLY SEQRES 5 A 98 ASP LEU GLU LYS PHE SER ARG VAL LEU VAL GLU GLN GLN SEQRES 6 A 98 GLN ASP ARG ALA ARG ARG GLU GLN GLU ARG ILE ARG LEU SEQRES 7 A 98 PHE SER ALA ASP PRO PHE ASP LEU GLU ALA GLN ALA LYS SEQRES 8 A 98 ILE GLU GLU ASP ILE ARG GLN HELIX 1 AA1 ASN A 20 ASN A 31 1 12 HELIX 2 AA2 ASN A 31 ASN A 42 1 12 HELIX 3 AA3 ASN A 42 SER A 51 1 10 HELIX 4 AA4 ASP A 53 ARG A 77 1 25 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