PDB Short entry for 5YDE HEADER TRANSCRIPTION 13-SEP-17 5YDE TITLE CRYSTAL STRUCTURE OF A DISEASE-RELATED GENE, HCDC73(1-111) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARAFIBROMIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-111; 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 5YDE 1 REMARK REVDAT 1 20-DEC-17 5YDE 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. 1.02 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 109711 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.119 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 5518 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 19.4030 - 3.1752 1.00 3458 192 0.1575 0.1706 REMARK 3 2 3.1752 - 2.5220 1.00 3478 189 0.1318 0.1410 REMARK 3 3 2.5220 - 2.2037 1.00 3509 171 0.1201 0.1296 REMARK 3 4 2.2037 - 2.0024 1.00 3457 185 0.1135 0.1375 REMARK 3 5 2.0024 - 1.8590 1.00 3520 172 0.1117 0.1393 REMARK 3 6 1.8590 - 1.7495 1.00 3450 188 0.1120 0.1264 REMARK 3 7 1.7495 - 1.6619 1.00 3518 177 0.1076 0.1319 REMARK 3 8 1.6619 - 1.5896 1.00 3489 145 0.1029 0.1483 REMARK 3 9 1.5896 - 1.5285 1.00 3482 201 0.0972 0.1270 REMARK 3 10 1.5285 - 1.4757 1.00 3490 182 0.0963 0.1134 REMARK 3 11 1.4757 - 1.4296 1.00 3497 196 0.0944 0.1203 REMARK 3 12 1.4296 - 1.3888 1.00 3479 163 0.1019 0.1322 REMARK 3 13 1.3888 - 1.3522 1.00 3414 212 0.1022 0.1248 REMARK 3 14 1.3522 - 1.3192 1.00 3511 150 0.1034 0.1207 REMARK 3 15 1.3192 - 1.2892 1.00 3482 169 0.0997 0.1388 REMARK 3 16 1.2892 - 1.2618 1.00 3493 226 0.0990 0.1011 REMARK 3 17 1.2618 - 1.2366 1.00 3458 171 0.1032 0.1273 REMARK 3 18 1.2366 - 1.2132 1.00 3484 182 0.0992 0.1397 REMARK 3 19 1.2132 - 1.1916 1.00 3476 203 0.1001 0.1302 REMARK 3 20 1.1916 - 1.1714 1.00 3524 154 0.1049 0.1206 REMARK 3 21 1.1714 - 1.1525 1.00 3450 189 0.1104 0.1148 REMARK 3 22 1.1525 - 1.1348 1.00 3455 220 0.1185 0.1600 REMARK 3 23 1.1348 - 1.1181 1.00 3444 191 0.1164 0.1388 REMARK 3 24 1.1181 - 1.1023 1.00 3559 178 0.1197 0.1364 REMARK 3 25 1.1023 - 1.0874 1.00 3422 200 0.1194 0.1423 REMARK 3 26 1.0874 - 1.0733 1.00 3397 207 0.1235 0.1360 REMARK 3 27 1.0733 - 1.0599 1.00 3542 170 0.1267 0.1508 REMARK 3 28 1.0599 - 1.0471 1.00 3479 185 0.1425 0.1727 REMARK 3 29 1.0471 - 1.0349 1.00 3460 150 0.1649 0.1627 REMARK 3 30 1.0349 - 1.0233 0.95 3316 200 0.1716 0.2090 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.100 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 : 0.011 978 REMARK 3 ANGLE : 1.505 1338 REMARK 3 CHIRALITY : 0.109 149 REMARK 3 PLANARITY : 0.010 172 REMARK 3 DIHEDRAL : 12.012 385 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 5YDE 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_1300005068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-16 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS 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 : 109711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 19.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.6100 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, TRIS, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.04550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.81300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.84150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.81300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.04550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.84150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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. (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 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 MET A 1 CG SD CE 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 ALA A 2 O HOH A 202 2.09 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 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 476 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 477 DISTANCE = 6.05 ANGSTROMS REMARK 525 HOH A 478 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 479 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A 480 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A 481 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 482 DISTANCE = 7.96 ANGSTROMS REMARK 525 HOH A 483 DISTANCE = 8.66 ANGSTROMS REMARK 525 HOH A 484 DISTANCE = 12.76 ANGSTROMS DBREF 5YDE A 1 111 UNP Q6P1J9 CDC73_HUMAN 1 111 SEQADV 5YDE GLY A 0 UNP Q6P1J9 EXPRESSION TAG SEQRES 1 A 112 GLY MET ALA ASP VAL LEU SER VAL LEU ARG GLN TYR ASN SEQRES 2 A 112 ILE GLN LYS LYS GLU ILE VAL VAL LYS GLY ASP GLU VAL SEQRES 3 A 112 ILE PHE GLY GLU PHE SER TRP PRO LYS ASN VAL LYS THR SEQRES 4 A 112 ASN TYR VAL VAL TRP GLY THR GLY LYS GLU GLY GLN PRO SEQRES 5 A 112 ARG GLU TYR TYR THR LEU ASP SER ILE LEU PHE LEU LEU SEQRES 6 A 112 ASN ASN VAL HIS LEU SER HIS PRO VAL TYR VAL ARG ARG SEQRES 7 A 112 ALA ALA THR GLU ASN ILE PRO VAL VAL ARG ARG PRO ASP SEQRES 8 A 112 ARG LYS ASP LEU LEU GLY TYR LEU ASN GLY GLU ALA SER SEQRES 9 A 112 THR SER ALA SER ILE ASP ARG SER FORMUL 2 HOH *284(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 ASN A 99 1 13 SHEET 1 AA1 3 VAL A 19 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 CRYST1 38.091 43.683 67.626 90.00 90.00 90.00 P 21 21 21 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 0.026253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022892 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014787 0.00000