HEADER SIGNALING PROTEIN 03-SEP-15 5DK8 TITLE HUMAN UBIQUITIN IN THE P1 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UBIQUITIN, UNP RESIDUES 2-75; COMPND 5 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET101D KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS,J.BACARIZO REVDAT 4 10-JAN-24 5DK8 1 REMARK LINK REVDAT 3 20-JAN-16 5DK8 1 JRNL REVDAT 2 13-JAN-16 5DK8 1 JRNL REVDAT 1 16-DEC-15 5DK8 0 JRNL AUTH A.CAMARA-ARTIGAS,M.PLAZA-GARRIDO,S.MARTINEZ-RODRIGUEZ, JRNL AUTH 2 J.BACARIZO JRNL TITL NEW CRYSTAL FORM OF HUMAN UBIQUITIN IN THE PRESENCE OF JRNL TITL 2 MAGNESIUM. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 72 29 2016 JRNL REFN ESSN 2053-230X JRNL PMID 26750481 JRNL DOI 10.1107/S2053230X15023390 REMARK 2 REMARK 2 RESOLUTION. 1.32 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.32 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 28709 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1458 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 27.8271 - 2.8430 0.97 2825 165 0.1841 0.1799 REMARK 3 2 2.8430 - 2.2569 0.95 2782 144 0.1913 0.2117 REMARK 3 3 2.2569 - 1.9717 0.94 2764 146 0.1671 0.1926 REMARK 3 4 1.9717 - 1.7915 0.93 2747 138 0.1624 0.1960 REMARK 3 5 1.7915 - 1.6631 0.93 2741 144 0.1652 0.2175 REMARK 3 6 1.6631 - 1.5650 0.94 2741 170 0.1653 0.2218 REMARK 3 7 1.5650 - 1.4867 0.92 2700 141 0.1602 0.2074 REMARK 3 8 1.4867 - 1.4220 0.91 2666 131 0.1779 0.2171 REMARK 3 9 1.4220 - 1.3672 0.90 2640 141 0.1900 0.2558 REMARK 3 10 1.3672 - 1.3200 0.89 2645 138 0.2215 0.2568 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.13 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 : 0.009 1189 REMARK 3 ANGLE : 1.217 1610 REMARK 3 CHIRALITY : 0.072 196 REMARK 3 PLANARITY : 0.006 207 REMARK 3 DIHEDRAL : 14.446 447 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 5DK8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : COMPOUND REFRACTIVE LENS MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.30 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.320 REMARK 200 RESOLUTION RANGE LOW (A) : 27.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4PIH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 30% W/V PEG 4000, 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 GLY B 75 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 11 CG CD CE NZ REMARK 470 GLN A 49 CG CD OE1 NE2 REMARK 470 ASN A 60 CG OD1 ND2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 11 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 74 CB CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 240 O HOH A 241 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O LYS B 33 NH2 ARG B 54 1455 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 204 O REMARK 620 2 HOH A 206 O 93.2 REMARK 620 3 HOH A 209 O 165.2 99.7 REMARK 620 4 HOH A 214 O 92.1 89.2 80.8 REMARK 620 5 HOH B 120 O 86.9 88.9 100.6 177.8 REMARK 620 6 HOH B 136 O 93.3 173.5 73.8 89.9 92.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 101 DBREF 5DK8 A 2 75 UNP P0CG47 UBB_HUMAN 2 75 DBREF 5DK8 B 2 75 UNP P0CG47 UBB_HUMAN 2 75 SEQADV 5DK8 HIS A 0 UNP P0CG47 EXPRESSION TAG SEQADV 5DK8 HIS A 1 UNP P0CG47 EXPRESSION TAG SEQADV 5DK8 HIS B 0 UNP P0CG47 EXPRESSION TAG SEQADV 5DK8 HIS B 1 UNP P0CG47 EXPRESSION TAG SEQRES 1 A 76 HIS HIS GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 A 76 ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN SEQRES 3 A 76 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 A 76 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU SEQRES 5 A 76 ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEQRES 6 A 76 SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 1 B 76 HIS HIS GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 B 76 ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN SEQRES 3 B 76 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 B 76 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU SEQRES 5 B 76 ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEQRES 6 B 76 SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY HET MG A 101 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *140(H2 O) HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 LEU A 56 ASN A 60 5 5 HELIX 4 AA4 THR B 22 GLY B 35 1 14 HELIX 5 AA5 PRO B 37 ASP B 39 5 3 HELIX 6 AA6 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 5 THR A 12 VAL A 17 0 SHEET 2 AA1 5 HIS A 1 THR A 7 -1 N HIS A 1 O VAL A 17 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 5 THR B 12 VAL B 17 0 SHEET 2 AA2 5 HIS B 1 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA2 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 AA2 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA2 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK MG MG A 101 O HOH A 204 1555 1555 2.09 LINK MG MG A 101 O HOH A 206 1555 1555 2.04 LINK MG MG A 101 O HOH A 209 1555 1555 2.08 LINK MG MG A 101 O HOH A 214 1555 1555 2.07 LINK MG MG A 101 O HOH B 120 1555 1556 1.98 LINK MG MG A 101 O HOH B 136 1555 1556 2.05 SITE 1 AC1 6 HOH A 204 HOH A 206 HOH A 209 HOH A 214 SITE 2 AC1 6 HOH B 120 HOH B 136 CRYST1 29.961 30.182 41.414 88.52 79.12 67.37 P 1 2 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 0.033377 -0.013914 -0.007148 0.00000 SCALE2 0.000000 0.035896 0.001859 0.00000 SCALE3 0.000000 0.000000 0.024622 0.00000