HEADER UNKNOWN FUNCTION 02-NOV-19 6L7Q TITLE CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN PYCH_01220 DERIVED FROM TITLE 2 PYROCOCCUS YAYANOSII COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS YAYANOSII (STRAIN CH1 / JCM 16557); SOURCE 3 ORGANISM_TAXID: 529709; SOURCE 4 STRAIN: CH1 / JCM 16557; SOURCE 5 GENE: PYCH_01220; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYTOSOLIC PROTEIN, UNKNOWN FUNCTION, HYPOTHETICAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.-H.JEON,H.NOH,B.-H.OH REVDAT 4 27-MAR-24 6L7Q 1 REMARK REVDAT 3 17-MAR-21 6L7Q 1 JRNL REVDAT 2 09-DEC-20 6L7Q 1 JRNL REVDAT 1 04-NOV-20 6L7Q 0 JRNL AUTH H.NOH,J.H.JEON,Y.G.KIM,B.H.OH JRNL TITL CRYSTAL STRUCTURE OF PYCH_01220 FROM PYROCOCCUS YAYANOSII JRNL TITL 2 POTENTIALLY INVOLVED IN BINDING NUCLEIC ACID. JRNL REF PROTEINS V. 89 468 2021 JRNL REFN ESSN 1097-0134 JRNL PMID 33236809 JRNL DOI 10.1002/PROT.26029 REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 3 NUMBER OF REFLECTIONS : 51395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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 23.9560 - 2.6547 0.83 4022 132 0.1971 0.2059 REMARK 3 2 2.6547 - 2.1075 0.80 3900 128 0.1953 0.2103 REMARK 3 3 2.1075 - 1.8412 0.76 3691 121 0.1861 0.1856 REMARK 3 4 1.8412 - 1.6729 0.99 4793 156 0.1824 0.2058 REMARK 3 5 1.6729 - 1.5530 0.97 4723 152 0.1711 0.2107 REMARK 3 6 1.5530 - 1.4615 0.95 4597 152 0.1743 0.1778 REMARK 3 7 1.4615 - 1.3883 0.93 4511 154 0.1757 0.1934 REMARK 3 8 1.3883 - 1.3279 0.89 4319 145 0.1833 0.2006 REMARK 3 9 1.3279 - 1.2767 0.83 4024 136 0.2140 0.2196 REMARK 3 10 1.2767 - 1.2327 0.80 3881 129 0.1996 0.2163 REMARK 3 11 1.2327 - 1.1942 0.76 3700 126 0.2390 0.2690 REMARK 3 12 1.1942 - 1.1600 0.74 3587 116 0.2197 0.2101 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.49 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6L7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014270. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-16 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 : 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) : 0.97943 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51395 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 23.956 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.26700 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: SAD REMARK 200 SOFTWARE USED: PHENIX 1.10.1_2155 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS (PH 8.5), 0.05M MAGNESIUM REMARK 280 SULFATE, 1.8M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.13900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.90631 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.81267 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 43.13900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.90631 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.81267 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 43.13900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.90631 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.81267 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.81263 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 41.62533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 49.81263 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 41.62533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 49.81263 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 41.62533 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 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 ARG A 14 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 202 O HOH A 312 2.08 REMARK 500 O HOH A 202 O HOH A 217 2.09 REMARK 500 NH2 ARG A 135 O HOH A 201 2.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 6L7Q A 1 144 UNP F8AFT0 F8AFT0_PYRYC 1 144 SEQADV 6L7Q MET A 0 UNP F8AFT0 INITIATING METHIONINE SEQRES 1 A 145 MET MET LEU LEU THR ARG HIS ALA LYS GLU ARG ILE ALA SEQRES 2 A 145 LYS ARG LEU ALA LYS LYS ARG SER LEU SER HIS ILE TYR SEQRES 3 A 145 SER SER LEU TRP ALA PHE LEU GLU ARG ALA VAL ARG ILE SEQRES 4 A 145 GLU ILE ALA GLU GLY VAL VAL ALA PHE THR ASP GLY ARG SEQRES 5 A 145 LYS THR LEU VAL CYS VAL PRO LEU ASP CYS GLU ARG LEU SEQRES 6 A 145 SER ARG GLY GLU ILE LEU GLU LYS VAL ARG GLY VAL GLY SEQRES 7 A 145 VAL TYR GLU CYS ILE PHE PRO GLU GLY ARG LEU ALA LYS SEQRES 8 A 145 LEU THR ARG PRO GLU LYS PHE LEU GLU SER VAL PRO PRO SEQRES 9 A 145 GLY GLU TYR TYR PHE TYR MET ASN ASP GLU LYS LYS VAL SEQRES 10 A 145 LEU TYR VAL GLY LYS ARG ARG PRO LEU LEU ALA ILE THR SEQRES 11 A 145 PHE ARG PRO ALA LYS ARG ASP GLU ARG LEU PHE TYR ILE SEQRES 12 A 145 TRP ALA FORMUL 2 HOH *184(H2 O) HELIX 1 AA1 THR A 4 ARG A 14 1 11 HELIX 2 AA2 SER A 20 ALA A 35 1 16 HELIX 3 AA3 ARG A 66 VAL A 73 1 8 HELIX 4 AA4 PRO A 84 ARG A 87 5 4 HELIX 5 AA5 ARG A 93 LEU A 98 1 6 HELIX 6 AA6 GLU A 99 VAL A 101 5 3 HELIX 7 AA7 LYS A 134 ALA A 144 1 11 SHEET 1 AA1 5 MET A 1 LEU A 3 0 SHEET 2 AA1 5 LEU A 125 PRO A 132 1 O ALA A 127 N LEU A 2 SHEET 3 AA1 5 LYS A 52 PRO A 58 -1 N THR A 53 O ARG A 131 SHEET 4 AA1 5 VAL A 44 THR A 48 -1 N VAL A 45 O CYS A 56 SHEET 5 AA1 5 VAL A 36 ALA A 41 -1 N ILE A 38 O ALA A 46 SHEET 1 AA2 5 GLU A 62 SER A 65 0 SHEET 2 AA2 5 GLU A 105 ASN A 111 -1 O TYR A 106 N LEU A 64 SHEET 3 AA2 5 VAL A 116 GLY A 120 -1 O GLY A 120 N TYR A 107 SHEET 4 AA2 5 TYR A 79 PHE A 83 1 N GLU A 80 O LEU A 117 SHEET 5 AA2 5 LEU A 88 THR A 92 -1 O LYS A 90 N CYS A 81 CRYST1 86.278 86.278 62.438 90.00 90.00 120.00 H 3 9 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 0.011590 0.006692 0.000000 0.00000 SCALE2 0.000000 0.013383 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016016 0.00000