HEADER TRANSCRIPTION 13-SEP-17 5YDF TITLE CRYSTAL STRUCTURE OF A DISEASE-RELATED GENE, HCDC73(1-100) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARAFIBROMIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-100; COMPND 5 SYNONYM: CELL DIVISION CYCLE PROTEIN 73 HOMOLOG,HYPERPARATHYROIDISM 2 COMPND 6 PROTEIN; COMPND 7 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: CDC73, C1ORF28, HRPT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TUMOR SUPPRESSOR, CANCER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR W.SUN,X.L.KUANG,Y.P.LIU,L.F.TIAN,X.X.YAN,W.Q.XU REVDAT 2 27-MAR-24 5YDF 1 REMARK REVDAT 1 20-DEC-17 5YDF 0 JRNL AUTH W.SUN,X.L.KUANG,Y.P.LIU,L.F.TIAN,X.X.YAN,W.XU JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN CDC73 JRNL TITL 2 AND ITS IMPLICATIONS FOR THE HYPERPARATHYROIDISM-JAW TUMOR JRNL TITL 3 (HPT-JT) SYNDROME JRNL REF SCI REP V. 7 15638 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29142233 JRNL DOI 10.1038/S41598-017-15715-9 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 38451 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1919 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 19.4912 - 3.3662 0.98 2664 141 0.1322 0.1516 REMARK 3 2 3.3662 - 2.6740 0.99 2626 143 0.1427 0.1867 REMARK 3 3 2.6740 - 2.3367 0.99 2616 140 0.1477 0.1696 REMARK 3 4 2.3367 - 2.1233 0.98 2624 130 0.1371 0.1724 REMARK 3 5 2.1233 - 1.9713 0.99 2632 136 0.1326 0.1806 REMARK 3 6 1.9713 - 1.8551 0.99 2625 118 0.1386 0.1839 REMARK 3 7 1.8551 - 1.7623 0.98 2589 130 0.1357 0.1770 REMARK 3 8 1.7623 - 1.6856 0.99 2603 128 0.1306 0.1988 REMARK 3 9 1.6856 - 1.6208 1.00 2683 130 0.1262 0.1690 REMARK 3 10 1.6208 - 1.5649 0.98 2569 142 0.1202 0.2008 REMARK 3 11 1.5649 - 1.5160 0.99 2576 142 0.1146 0.1738 REMARK 3 12 1.5160 - 1.4726 0.99 2656 125 0.1195 0.1745 REMARK 3 13 1.4726 - 1.4339 0.99 2564 168 0.1286 0.1806 REMARK 3 14 1.4339 - 1.3989 0.95 2505 146 0.1466 0.2145 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.012 1709 REMARK 3 ANGLE : 1.361 2335 REMARK 3 CHIRALITY : 0.063 259 REMARK 3 PLANARITY : 0.008 299 REMARK 3 DIHEDRAL : 12.904 660 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 5YDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-16; 02-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRF; SSRF REMARK 200 BEAMLINE : BL19U1; BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785; 0.9785 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M; DECTRIS REMARK 200 PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38451 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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; 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 (%): 42.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TRIS, MAGNESIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.75200 REMARK 290 SMTRY3 2 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 A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 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 GLU B 48 OE2 REMARK 470 GLN B 50 CD OE1 NE2 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 B 298 O HOH B 302 1.93 REMARK 500 O HOH A 241 O HOH A 318 1.98 REMARK 500 O HOH B 225 O HOH B 321 1.99 REMARK 500 O HOH A 227 O HOH A 364 2.01 REMARK 500 O HOH A 262 O HOH A 317 2.07 REMARK 500 O HOH A 371 O HOH B 350 2.10 REMARK 500 O HOH A 309 O HOH A 355 2.12 REMARK 500 O HOH B 281 O HOH B 323 2.12 REMARK 500 O HOH B 303 O HOH B 323 2.16 REMARK 500 O HOH B 296 O HOH B 314 2.16 REMARK 500 O HOH B 303 O HOH B 352 2.19 REMARK 500 O HOH A 281 O HOH A 337 2.19 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 HOH A 305 O HOH A 330 2746 1.88 REMARK 500 O HOH B 287 O HOH B 293 1455 2.07 REMARK 500 O HOH A 318 O HOH A 332 2756 2.09 REMARK 500 O HOH A 354 O HOH A 364 1655 2.10 REMARK 500 O HOH A 364 O HOH A 375 1455 2.14 REMARK 500 O HOH A 342 O HOH A 364 1655 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 29 CD GLU A 29 OE2 -0.086 REMARK 500 GLU B 29 CD GLU B 29 OE1 -0.072 REMARK 500 REMARK 500 REMARK: NULL DBREF 5YDF A 1 100 UNP Q6P1J9 CDC73_HUMAN 1 100 DBREF 5YDF B 1 100 UNP Q6P1J9 CDC73_HUMAN 1 100 SEQADV 5YDF GLY A 0 UNP Q6P1J9 EXPRESSION TAG SEQADV 5YDF GLY B 0 UNP Q6P1J9 EXPRESSION TAG SEQRES 1 A 101 GLY MET ALA ASP VAL LEU SER VAL LEU ARG GLN TYR ASN SEQRES 2 A 101 ILE GLN LYS LYS GLU ILE VAL VAL LYS GLY ASP GLU VAL SEQRES 3 A 101 ILE PHE GLY GLU PHE SER TRP PRO LYS ASN VAL LYS THR SEQRES 4 A 101 ASN TYR VAL VAL TRP GLY THR GLY LYS GLU GLY GLN PRO SEQRES 5 A 101 ARG GLU TYR TYR THR LEU ASP SER ILE LEU PHE LEU LEU SEQRES 6 A 101 ASN ASN VAL HIS LEU SER HIS PRO VAL TYR VAL ARG ARG SEQRES 7 A 101 ALA ALA THR GLU ASN ILE PRO VAL VAL ARG ARG PRO ASP SEQRES 8 A 101 ARG LYS ASP LEU LEU GLY TYR LEU ASN GLY SEQRES 1 B 101 GLY MET ALA ASP VAL LEU SER VAL LEU ARG GLN TYR ASN SEQRES 2 B 101 ILE GLN LYS LYS GLU ILE VAL VAL LYS GLY ASP GLU VAL SEQRES 3 B 101 ILE PHE GLY GLU PHE SER TRP PRO LYS ASN VAL LYS THR SEQRES 4 B 101 ASN TYR VAL VAL TRP GLY THR GLY LYS GLU GLY GLN PRO SEQRES 5 B 101 ARG GLU TYR TYR THR LEU ASP SER ILE LEU PHE LEU LEU SEQRES 6 B 101 ASN ASN VAL HIS LEU SER HIS PRO VAL TYR VAL ARG ARG SEQRES 7 B 101 ALA ALA THR GLU ASN ILE PRO VAL VAL ARG ARG PRO ASP SEQRES 8 B 101 ARG LYS ASP LEU LEU GLY TYR LEU ASN GLY FORMUL 3 HOH *348(H2 O) HELIX 1 AA1 ASP A 3 LYS A 15 1 13 HELIX 2 AA2 LEU A 57 ASN A 66 1 10 HELIX 3 AA3 SER A 70 ASN A 82 1 13 HELIX 4 AA4 ARG A 87 GLY A 100 1 14 HELIX 5 AA5 VAL B 4 LYS B 15 1 12 HELIX 6 AA6 LEU B 57 ASN B 66 1 10 HELIX 7 AA7 SER B 70 ASN B 82 1 13 HELIX 8 AA8 ARG B 87 GLY B 100 1 14 SHEET 1 AA1 3 ILE A 18 LYS A 21 0 SHEET 2 AA1 3 GLU A 24 PHE A 27 -1 O ILE A 26 N VAL A 19 SHEET 3 AA1 3 PHE A 30 PRO A 33 -1 O TRP A 32 N VAL A 25 SHEET 1 AA2 2 LYS A 37 VAL A 41 0 SHEET 2 AA2 2 TYR A 54 THR A 56 -1 O TYR A 55 N THR A 38 SHEET 1 AA3 3 ILE B 18 LYS B 21 0 SHEET 2 AA3 3 GLU B 24 PHE B 27 -1 O ILE B 26 N VAL B 19 SHEET 3 AA3 3 PHE B 30 PRO B 33 -1 O TRP B 32 N VAL B 25 SHEET 1 AA4 2 LYS B 37 VAL B 41 0 SHEET 2 AA4 2 TYR B 54 THR B 56 -1 O TYR B 55 N THR B 38 CRYST1 28.590 53.504 65.734 90.00 95.66 90.00 P 1 21 1 4 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 0.034977 0.000000 0.003467 0.00000 SCALE2 0.000000 0.018690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015287 0.00000