HEADER UNKNOWN FUNCTION 30-JAN-24 8VVA TITLE STRUCTURE OF DUF1480 DOMAIN-CONTAINING PROTEIN FROM KLEBSIELLA TITLE 2 PNEUMONIAE SUBSP. PNEUMONIAE SA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF1480 DOMAIN-CONTAINING PROTEIN, YEBV FAMILY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BB784_10290; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DUF1480, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR C.SEMPER,A.SAVCHENKO,N.WATANABE,CENTER FOR STRUCTURAL BIOLOGY OF AUTHOR 2 INFECTIOUS DISEASES (CSBID) REVDAT 1 19-JUN-24 8VVA 0 JRNL AUTH C.SEMPER,A.SAVCHENKO,N.WATANABE, JRNL AUTH 2 CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES (CSBID) JRNL TITL STRUCTURE OF DUF1480 DOMAIN-CONTAINING PROTEIN FROM JRNL TITL 2 KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE SA1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 41.5300 - 4.2200 0.98 1403 154 0.1943 0.2041 REMARK 3 2 4.2200 - 3.3500 1.00 1344 147 0.1763 0.2301 REMARK 3 3 3.3500 - 2.9200 1.00 1330 145 0.2096 0.2565 REMARK 3 4 2.9200 - 2.6600 1.00 1310 144 0.2208 0.2305 REMARK 3 5 2.6600 - 2.4700 1.00 1311 142 0.2225 0.2748 REMARK 3 6 2.4700 - 2.3200 1.00 1292 143 0.2135 0.2651 REMARK 3 7 2.3200 - 2.2000 1.00 1306 141 0.2041 0.2604 REMARK 3 8 2.2000 - 2.1100 1.00 1295 142 0.2059 0.2552 REMARK 3 9 2.1100 - 2.0300 0.99 1272 135 0.2183 0.2438 REMARK 3 10 2.0300 - 1.9600 1.00 1281 141 0.2067 0.2193 REMARK 3 11 1.9600 - 1.9000 0.98 1263 138 0.2393 0.2656 REMARK 3 12 1.9000 - 1.8400 1.00 1279 140 0.2344 0.2300 REMARK 3 13 1.8400 - 1.7900 0.99 1255 137 0.2457 0.2793 REMARK 3 14 1.7900 - 1.7500 0.98 1278 140 0.2801 0.2976 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.206 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.431 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 1249 REMARK 3 ANGLE : 0.883 1695 REMARK 3 CHIRALITY : 0.057 182 REMARK 3 PLANARITY : 0.005 224 REMARK 3 DIHEDRAL : 2.745 749 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8VVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20271 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350/0.1M CITRIC ACID PH 3.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.24600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.29550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.29550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.62300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.29550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.29550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.86900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.29550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.29550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.62300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.29550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.29550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.86900 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 31.24600 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A 1 REMARK 465 MSE B 1 REMARK 465 SER B 2 REMARK 465 LYS B 3 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 HIS A 66 137.26 -170.19 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8VVA A 1 79 UNP A0AA34SSY7_KLEPN DBREF2 8VVA A A0AA34SSY7 24 102 DBREF1 8VVA B 1 79 UNP A0AA34SSY7_KLEPN DBREF2 8VVA B A0AA34SSY7 24 102 SEQRES 1 A 79 MSE SER LYS THR ASN VAL ARG ILE GLY ALA PHE GLU ILE SEQRES 2 A 79 ASP ASP ALA GLU LEU HIS GLY GLU HIS GLN GLY GLU ARG SEQRES 3 A 79 THR LEU SER ILE PRO CYS LYS SER ASP PRO ASP LEU CYS SEQRES 4 A 79 MSE GLN LEU ASP ALA TRP ASP ALA ASP THR SER VAL PRO SEQRES 5 A 79 ALA ILE LEU ASN GLY GLU HIS SER VAL LEU TYR ARG LYS SEQRES 6 A 79 HIS TYR ASP ARG GLN SER ASP ALA TRP VAL MSE ARG LEU SEQRES 7 A 79 ALA SEQRES 1 B 79 MSE SER LYS THR ASN VAL ARG ILE GLY ALA PHE GLU ILE SEQRES 2 B 79 ASP ASP ALA GLU LEU HIS GLY GLU HIS GLN GLY GLU ARG SEQRES 3 B 79 THR LEU SER ILE PRO CYS LYS SER ASP PRO ASP LEU CYS SEQRES 4 B 79 MSE GLN LEU ASP ALA TRP ASP ALA ASP THR SER VAL PRO SEQRES 5 B 79 ALA ILE LEU ASN GLY GLU HIS SER VAL LEU TYR ARG LYS SEQRES 6 B 79 HIS TYR ASP ARG GLN SER ASP ALA TRP VAL MSE ARG LEU SEQRES 7 B 79 ALA MODRES 8VVA MSE A 40 MET MODIFIED RESIDUE MODRES 8VVA MSE A 76 MET MODIFIED RESIDUE MODRES 8VVA MSE B 40 MET MODIFIED RESIDUE MODRES 8VVA MSE B 76 MET MODIFIED RESIDUE HET MSE A 40 8 HET MSE A 76 8 HET MSE B 40 8 HET MSE B 76 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *65(H2 O) HELIX 1 AA1 ASP A 35 ALA A 44 1 10 HELIX 2 AA2 ASP B 35 TRP B 45 1 11 SHEET 1 AA1 7 PHE A 11 ILE A 13 0 SHEET 2 AA1 7 VAL A 6 ILE A 8 -1 N VAL A 6 O ILE A 13 SHEET 3 AA1 7 VAL A 51 LEU A 55 -1 O ILE A 54 N ARG A 7 SHEET 4 AA1 7 GLU A 58 ASP A 68 -1 O LEU A 62 N VAL A 51 SHEET 5 AA1 7 ALA A 73 LEU A 78 -1 O ARG A 77 N TYR A 63 SHEET 6 AA1 7 THR A 27 PRO A 31 -1 N LEU A 28 O MSE A 76 SHEET 7 AA1 7 GLU A 17 LEU A 18 -1 N GLU A 17 O SER A 29 SHEET 1 AA2 7 PHE B 11 ILE B 13 0 SHEET 2 AA2 7 VAL B 6 ILE B 8 -1 N VAL B 6 O ILE B 13 SHEET 3 AA2 7 VAL B 51 LEU B 55 -1 O ILE B 54 N ARG B 7 SHEET 4 AA2 7 GLU B 58 ASP B 68 -1 O SER B 60 N ALA B 53 SHEET 5 AA2 7 ALA B 73 LEU B 78 -1 O ARG B 77 N TYR B 63 SHEET 6 AA2 7 GLU B 25 PRO B 31 -1 N LEU B 28 O MSE B 76 SHEET 7 AA2 7 GLU B 17 HIS B 22 -1 N HIS B 22 O GLU B 25 SSBOND 1 CYS A 32 CYS A 39 1555 1555 2.05 SSBOND 2 CYS B 32 CYS B 39 1555 1555 2.06 LINK C CYS A 39 N MSE A 40 1555 1555 1.33 LINK C MSE A 40 N GLN A 41 1555 1555 1.34 LINK C VAL A 75 N MSE A 76 1555 1555 1.33 LINK C MSE A 76 N ARG A 77 1555 1555 1.32 LINK C CYS B 39 N MSE B 40 1555 1555 1.33 LINK C MSE B 40 N GLN B 41 1555 1555 1.33 LINK C VAL B 75 N MSE B 76 1555 1555 1.33 LINK C MSE B 76 N ARG B 77 1555 1555 1.33 CRYST1 78.591 78.591 62.492 90.00 90.00 90.00 P 41 21 2 16 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 0.012724 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016002 0.00000