HEADER HYDROLASE 26-JUN-16 5KM6 TITLE HUMAN HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT1) H112N TITLE 2 MUTANT ARA-A NUCLEOSIDE PHOSPHORAMIDATE SUBSTRATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADENOSINE 5'-MONOPHOSPHORAMIDASE; COMPND 5 EC: 3.-.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HINT1, HINT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS HINT, HISTIDINE TRIAD, HIT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.MAIZE,B.C.FINZEL REVDAT 5 27-SEP-23 5KM6 1 JRNL REVDAT 4 15-NOV-17 5KM6 1 JRNL REVDAT 3 18-OCT-17 5KM6 1 JRNL REVDAT 2 26-JUL-17 5KM6 1 JRNL REVDAT 1 28-JUN-17 5KM6 0 JRNL AUTH K.M.MAIZE,R.SHAH,A.STROM,S.KUMARAPPERUMA,A.ZHOU,C.R.WAGNER, JRNL AUTH 2 B.C.FINZEL JRNL TITL A CRYSTAL STRUCTURE BASED GUIDE TO THE DESIGN OF HUMAN JRNL TITL 2 HISTIDINE TRIAD NUCLEOTIDE BINDING PROTEIN 1 (HHINT1) JRNL TITL 3 ACTIVATED PROTIDES. JRNL REF MOL. PHARM. V. 14 3987 2017 JRNL REFN ESSN 1543-8392 JRNL PMID 28968488 JRNL DOI 10.1021/ACS.MOLPHARMACEUT.7B00664 REMARK 2 REMARK 2 RESOLUTION. 1.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16477 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 791 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 35.0972 - 2.9069 1.00 2825 128 0.1706 0.1798 REMARK 3 2 2.9069 - 2.3075 1.00 2636 137 0.1859 0.2114 REMARK 3 3 2.3075 - 2.0158 1.00 2585 120 0.1664 0.1909 REMARK 3 4 2.0158 - 1.8315 1.00 2555 120 0.1628 0.1787 REMARK 3 5 1.8315 - 1.7002 1.00 2562 145 0.1641 0.2088 REMARK 3 6 1.7002 - 1.6000 1.00 2523 141 0.1687 0.1895 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 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 : 0.007 922 REMARK 3 ANGLE : 1.376 1252 REMARK 3 CHIRALITY : 0.054 135 REMARK 3 PLANARITY : 0.006 158 REMARK 3 DIHEDRAL : 13.899 342 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 5KM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 144.239 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 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 2.5.6 REMARK 200 STARTING MODEL: 1KPF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 32% PEG 8000, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 72.11950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.08150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.08150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.17925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.08150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.08150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.05975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.08150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.08150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.17925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.08150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.08150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.05975 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 72.11950 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: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 4 REMARK 465 ILE A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 GLN A 9 REMARK 465 VAL A 10 REMARK 465 ALA A 11 REMARK 465 ARG A 12 REMARK 465 PRO A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 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 A 26 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6US A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TW2 RELATED DB: PDB REMARK 900 RELATED ID: 5IPB RELATED DB: PDB REMARK 900 RELATED ID: 5IPC RELATED DB: PDB REMARK 900 RELATED ID: 5IPD RELATED DB: PDB REMARK 900 RELATED ID: 5IPE RELATED DB: PDB REMARK 900 RELATED ID: 5KLY RELATED DB: PDB REMARK 900 RELATED ID: 5KLZ RELATED DB: PDB REMARK 900 RELATED ID: 5KM0 RELATED DB: PDB REMARK 900 RELATED ID: 5KM1 RELATED DB: PDB REMARK 900 RELATED ID: 5KM2 RELATED DB: PDB REMARK 900 RELATED ID: 5KM3 RELATED DB: PDB REMARK 900 RELATED ID: 5KM4 RELATED DB: PDB REMARK 900 RELATED ID: 5KM5 RELATED DB: PDB REMARK 900 RELATED ID: 5KM7 RELATED DB: PDB REMARK 900 RELATED ID: 5KM8 RELATED DB: PDB REMARK 900 RELATED ID: 5KM9 RELATED DB: PDB REMARK 900 RELATED ID: 5KMA RELATED DB: PDB REMARK 900 RELATED ID: 5KMB RELATED DB: PDB REMARK 900 RELATED ID: 5KMC RELATED DB: PDB DBREF 5KM6 A 1 126 UNP P49773 HINT1_HUMAN 1 126 SEQADV 5KM6 SER A -2 UNP P49773 EXPRESSION TAG SEQADV 5KM6 ASN A -1 UNP P49773 EXPRESSION TAG SEQADV 5KM6 ALA A 0 UNP P49773 EXPRESSION TAG SEQADV 5KM6 ASN A 112 UNP P49773 HIS 112 ENGINEERED MUTATION SEQRES 1 A 129 SER ASN ALA MET ALA ASP GLU ILE ALA LYS ALA GLN VAL SEQRES 2 A 129 ALA ARG PRO GLY GLY ASP THR ILE PHE GLY LYS ILE ILE SEQRES 3 A 129 ARG LYS GLU ILE PRO ALA LYS ILE ILE PHE GLU ASP ASP SEQRES 4 A 129 ARG CYS LEU ALA PHE HIS ASP ILE SER PRO GLN ALA PRO SEQRES 5 A 129 THR HIS PHE LEU VAL ILE PRO LYS LYS HIS ILE SER GLN SEQRES 6 A 129 ILE SER VAL ALA GLU ASP ASP ASP GLU SER LEU LEU GLY SEQRES 7 A 129 HIS LEU MET ILE VAL GLY LYS LYS CYS ALA ALA ASP LEU SEQRES 8 A 129 GLY LEU ASN LYS GLY TYR ARG MET VAL VAL ASN GLU GLY SEQRES 9 A 129 SER ASP GLY GLY GLN SER VAL TYR HIS VAL ASN LEU HIS SEQRES 10 A 129 VAL LEU GLY GLY ARG GLN MET HIS TRP PRO PRO GLY HET 6US A 201 34 HETNAM 6US [(2~{R},3~{S},4~{S},5~{R})-5-(6-AMINOPURIN-9-YL)-3,4- HETNAM 2 6US BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-~{N}-[2-(1~{H}-INDOL- HETNAM 3 6US 3-YL)ETHYL]PHOSPHONAMIDIC ACID HETSYN 6US TPARA-AD FORMUL 2 6US C20 H24 N7 O6 P FORMUL 3 HOH *92(H2 O) HELIX 1 AA1 THR A 17 ARG A 24 1 8 HELIX 2 AA2 GLN A 62 ALA A 66 5 5 HELIX 3 AA3 GLU A 67 ASP A 69 5 3 HELIX 4 AA4 ASP A 70 LEU A 88 1 19 HELIX 5 AA5 GLU A 100 GLY A 105 1 6 SHEET 1 AA1 5 ILE A 31 GLU A 34 0 SHEET 2 AA1 5 CYS A 38 HIS A 42 -1 O ALA A 40 N ILE A 32 SHEET 3 AA1 5 THR A 50 PRO A 56 -1 O LEU A 53 N PHE A 41 SHEET 4 AA1 5 LEU A 113 GLY A 117 -1 O LEU A 113 N VAL A 54 SHEET 5 AA1 5 TYR A 94 VAL A 98 -1 N VAL A 97 O HIS A 114 CISPEP 1 TRP A 123 PRO A 124 0 1.92 SITE 1 AC1 23 PHE A 19 LYS A 25 GLU A 34 PHE A 41 SITE 2 AC1 23 HIS A 42 ASP A 43 ILE A 44 ASN A 99 SITE 3 AC1 23 GLY A 105 GLN A 106 SER A 107 VAL A 108 SITE 4 AC1 23 ASN A 112 HIS A 114 MET A 121 TRP A 123 SITE 5 AC1 23 HOH A 307 HOH A 314 HOH A 317 HOH A 322 SITE 6 AC1 23 HOH A 324 HOH A 334 HOH A 337 CRYST1 40.163 40.163 144.239 90.00 90.00 90.00 P 43 21 2 8 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 0.024899 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024899 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006933 0.00000