HEADER HYDROLASE 31-MAY-23 8JJZ TITLE CRYSTAL STRUCTURE OF QQ-HNTAQ1 C28S COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN N-TERMINAL GLUTAMINE AMIDOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GLN-2 AND GLN-1 ARE ADDED TO THE N-TERMINUS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C8ORF32; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KANG,B.W.HAN REVDAT 1 26-JUN-24 8JJZ 0 JRNL AUTH J.M.KANG,J.S.PARK,J.S.LEE,J.Y.JANG,B.W.HAN JRNL TITL STRUCTURAL STUDY FOR SUBSTRATE RECOGNITION OF HUMAN JRNL TITL 2 N-TERMINAL GLUTAMINE AMIDOHYDROLASE 1 IN THE ARGININE JRNL TITL 3 N-DEGRON PATHWAY. JRNL REF PROTEIN SCI. V. 33 E5067 2024 JRNL REFN ESSN 1469-896X JRNL PMID 38864716 JRNL DOI 10.1002/PRO.5067 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 3 NUMBER OF REFLECTIONS : 12817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 642 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 40.3100 - 3.4700 0.99 2863 152 0.1670 0.1796 REMARK 3 2 3.4700 - 2.7500 1.00 2860 151 0.1762 0.2320 REMARK 3 3 2.7500 - 2.4100 0.93 2620 138 0.2023 0.2526 REMARK 3 4 2.4100 - 2.1900 0.73 2079 109 0.2034 0.2719 REMARK 3 5 2.1900 - 2.0300 0.62 1753 92 0.2129 0.2870 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.581 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.13 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 : 0.003 1709 REMARK 3 ANGLE : 0.619 2329 REMARK 3 CHIRALITY : 0.048 235 REMARK 3 PLANARITY : 0.008 307 REMARK 3 DIHEDRAL : 17.760 226 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 8JJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038082. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-20 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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14806 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M TRIS PH 8.5, AND 25 % (W/V) POLYETHYLENE GLYCOL (PEG) 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.15K 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 32.28700 REMARK 290 SMTRY3 2 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 3 REMARK 465 ASN A 4 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 ALA A 8 58.10 -99.86 REMARK 500 ASP A 43 53.57 -108.77 REMARK 500 SER A 56 -168.82 -167.55 REMARK 500 ARG A 70 75.47 -150.77 REMARK 500 LYS A 117 171.43 59.48 REMARK 500 ASP A 151 -158.74 -91.47 REMARK 500 MET A 173 103.87 -165.74 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 434 DISTANCE = 8.45 ANGSTROMS REMARK 525 HOH A 435 DISTANCE = 9.90 ANGSTROMS DBREF1 8JJZ A 1 202 UNP A0A024R9I8_HUMAN DBREF2 8JJZ A A0A024R9I8 1 202 SEQADV 8JJZ GLN A -1 UNP A0A024R9I EXPRESSION TAG SEQADV 8JJZ GLN A 0 UNP A0A024R9I EXPRESSION TAG SEQADV 8JJZ SER A 28 UNP A0A024R9I CYS 28 ENGINEERED MUTATION SEQADV 8JJZ SER A 93 UNP A0A024R9I ASN 93 VARIANT SEQADV 8JJZ ILE A 116 UNP A0A024R9I PHE 116 VARIANT SEQADV 8JJZ CYS A 134 UNP A0A024R9I ARG 134 VARIANT SEQRES 1 A 204 GLN GLN MET GLU GLY ASN GLY PRO ALA ALA VAL HIS TYR SEQRES 2 A 204 GLN PRO ALA SER PRO PRO ARG ASP ALA CYS VAL TYR SER SEQRES 3 A 204 SER CYS TYR SER GLU GLU ASN VAL TRP LYS LEU CYS GLU SEQRES 4 A 204 TYR ILE LYS ASN HIS ASP GLN TYR PRO LEU GLU GLU CYS SEQRES 5 A 204 TYR ALA VAL PHE ILE SER ASN GLU ARG LYS MET ILE PRO SEQRES 6 A 204 ILE TRP LYS GLN GLN ALA ARG PRO GLY ASP GLY PRO VAL SEQRES 7 A 204 ILE TRP ASP TYR HIS VAL VAL LEU LEU HIS VAL SER SER SEQRES 8 A 204 GLY GLY GLN SER PHE ILE TYR ASP LEU ASP THR VAL LEU SEQRES 9 A 204 PRO PHE PRO CYS LEU PHE ASP THR TYR VAL GLU ASP ALA SEQRES 10 A 204 ILE LYS SER ASP ASP ASP ILE HIS PRO GLN PHE ARG ARG SEQRES 11 A 204 LYS PHE ARG VAL ILE CYS ALA ASP SER TYR LEU LYS ASN SEQRES 12 A 204 PHE ALA SER ASP ARG SER HIS MET LYS ASP SER SER GLY SEQRES 13 A 204 ASN TRP ARG GLU PRO PRO PRO PRO TYR PRO CYS ILE GLU SEQRES 14 A 204 THR GLY ASP SER LYS MET ASN LEU ASN ASP PHE ILE SER SEQRES 15 A 204 MET ASP PRO LYS VAL GLY TRP GLY ALA VAL TYR THR LEU SEQRES 16 A 204 SER GLU PHE THR HIS ARG PHE GLY SER FORMUL 2 HOH *135(H2 O) HELIX 1 AA1 PRO A 17 CYS A 21 5 5 HELIX 2 AA2 TYR A 27 HIS A 42 1 16 HELIX 3 AA3 PRO A 46 GLU A 48 5 3 HELIX 4 AA4 PHE A 108 ALA A 115 1 8 HELIX 5 AA5 HIS A 123 ARG A 127 5 5 HELIX 6 AA6 ALA A 135 PHE A 142 1 8 HELIX 7 AA7 ARG A 146 LYS A 150 5 5 HELIX 8 AA8 LEU A 175 SER A 180 1 6 HELIX 9 AA9 LEU A 193 GLY A 201 1 9 SHEET 1 AA1 6 CYS A 106 LEU A 107 0 SHEET 2 AA1 6 SER A 93 TYR A 96 -1 N ILE A 95 O CYS A 106 SHEET 3 AA1 6 HIS A 81 VAL A 87 -1 N LEU A 84 O TYR A 96 SHEET 4 AA1 6 CYS A 50 SER A 56 -1 N ILE A 55 O HIS A 81 SHEET 5 AA1 6 LYS A 129 CYS A 134 -1 O ILE A 133 N ALA A 52 SHEET 6 AA1 6 ALA A 189 THR A 192 -1 O TYR A 191 N PHE A 130 SHEET 1 AA2 2 ILE A 62 ILE A 64 0 SHEET 2 AA2 2 VAL A 76 TRP A 78 -1 O TRP A 78 N ILE A 62 CISPEP 1 PHE A 104 PRO A 105 0 -0.21 CRYST1 40.613 64.574 44.927 90.00 97.02 90.00 P 1 21 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 0.024623 0.000000 0.003032 0.00000 SCALE2 0.000000 0.015486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022426 0.00000