HEADER HYDROLASE 13-FEB-18 5ZBY TITLE CRYSTAL STRUCTURE OF A [NIFE] HYDROGENASE MATURATION PROTEASE HYCI TITLE 2 FROM THERMOCOCCUS KODAKARENSIS KOD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE MATURATION PROTEASE HYCI; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS KOD1; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK2004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MATURATION PROTEASE, HYCI, [NIFE] HYDROGENASE, C-TERMINAL CLEAVAGE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KWON,Y.NISHITANI,K.MIKI REVDAT 3 22-NOV-23 5ZBY 1 REMARK REVDAT 2 04-APR-18 5ZBY 1 JRNL REVDAT 1 28-MAR-18 5ZBY 0 JRNL AUTH S.KWON,Y.NISHITANI,Y.HIRAO,T.KANAI,H.ATOMI,K.MIKI JRNL TITL STRUCTURE OF A [NIFE] HYDROGENASE MATURATION PROTEASE HYCI JRNL TITL 2 PROVIDES INSIGHTS INTO ITS SUBSTRATE SELECTIVITY JRNL REF BIOCHEM. BIOPHYS. RES. V. 498 782 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29526754 JRNL DOI 10.1016/J.BBRC.2018.03.058 REMARK 2 REMARK 2 RESOLUTION. 1.59 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 25672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1254 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 47.6489 - 3.3091 1.00 3005 146 0.1815 0.2073 REMARK 3 2 3.3091 - 2.6266 1.00 2805 159 0.2032 0.2288 REMARK 3 3 2.6266 - 2.2946 1.00 2758 154 0.2111 0.1969 REMARK 3 4 2.2946 - 2.0848 1.00 2752 148 0.2100 0.2223 REMARK 3 5 2.0848 - 1.9353 1.00 2734 137 0.2118 0.2345 REMARK 3 6 1.9353 - 1.8212 0.99 2719 134 0.2291 0.2500 REMARK 3 7 1.8212 - 1.7300 1.00 2724 122 0.2538 0.3135 REMARK 3 8 1.7300 - 1.6547 0.99 2687 139 0.2714 0.3294 REMARK 3 9 1.6547 - 1.5910 0.83 2234 115 0.3061 0.3369 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.410 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 : 0.015 1201 REMARK 3 ANGLE : 1.632 1626 REMARK 3 CHIRALITY : 0.088 197 REMARK 3 PLANARITY : 0.009 208 REMARK 3 DIHEDRAL : 13.440 450 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 5ZBY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1300006828. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25807 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.591 REMARK 200 RESOLUTION RANGE LOW (A) : 47.628 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.62300 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: 2E85 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES (PH 7.5), 2-METHYL-2,4 REMARK 280 -PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 73.08350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.18850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.18850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.54175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.18850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.18850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 109.62525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.18850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.18850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.54175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.18850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.18850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 109.62525 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 73.08350 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 MET A 1 REMARK 465 LYS A 158 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 HIS A 101 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 156 CG CD CE NZ 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 372 O HOH A 379 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 200 DBREF 5ZBY A 1 158 UNP Q5JIH7 Q5JIH7_THEKO 1 158 SEQRES 1 A 158 MET SER VAL LEU GLU ASP VAL PHE SER GLY LYS THR ARG SEQRES 2 A 158 ILE VAL ILE CYS GLY ILE GLY ASN ASP VAL ARG GLY ASP SEQRES 3 A 158 ASP ALA PHE GLY VAL LEU VAL ALA GLU ARG LEU LYS GLU SEQRES 4 A 158 LEU VAL LYS THR PRO ASP VAL LEU ILE LEU ASN CYS GLY SEQRES 5 A 158 GLU MET PRO GLU SER TYR VAL GLY LYS ILE ALA ALA PHE SEQRES 6 A 158 LYS PRO ASP LEU VAL VAL PHE VAL ASP ALA ILE HIS PHE SEQRES 7 A 158 GLY GLY GLU ILE GLY GLU PHE ILE ILE ALA ASP PRO LEU SEQRES 8 A 158 LYS THR LEU GLY GLU ALA VAL SER THR HIS GLY LEU PRO SEQRES 9 A 158 LEU ARG ILE VAL ALA SER TYR ILE LYS GLU GLN THR GLY SEQRES 10 A 158 SER ASP ILE VAL LEU ILE GLY CYS GLN PRO GLY SER THR SEQRES 11 A 158 GLY LEU PHE GLU GLU PRO SER GLU LEU ILE LYS GLU ARG SEQRES 12 A 158 ALA GLU ARG LEU ALA GLU LEU ILE ALA GLU ILE LEU LYS SEQRES 13 A 158 ASN LYS HET EPE A 200 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 EPE C8 H18 N2 O4 S FORMUL 3 HOH *102(H2 O) HELIX 1 AA1 SER A 2 SER A 9 1 8 HELIX 2 AA2 ARG A 24 ASP A 27 5 4 HELIX 3 AA3 ALA A 28 VAL A 41 1 14 HELIX 4 AA4 MET A 54 SER A 57 5 4 HELIX 5 AA5 TYR A 58 PHE A 65 1 8 HELIX 6 AA6 PRO A 104 GLY A 117 1 14 HELIX 7 AA7 SER A 137 ASN A 157 1 21 SHEET 1 AA1 5 VAL A 46 ASN A 50 0 SHEET 2 AA1 5 ILE A 14 GLY A 18 1 N GLY A 18 O LEU A 49 SHEET 3 AA1 5 LEU A 69 ALA A 75 1 O VAL A 71 N CYS A 17 SHEET 4 AA1 5 ASP A 119 CYS A 125 1 O ILE A 123 N PHE A 72 SHEET 5 AA1 5 PHE A 85 ALA A 88 -1 N ALA A 88 O LEU A 122 SITE 1 AC1 14 ILE A 19 GLY A 20 ARG A 24 ASP A 27 SITE 2 AC1 14 ASP A 74 ALA A 75 THR A 100 HIS A 101 SITE 3 AC1 14 PRO A 104 LEU A 105 HOH A 331 HOH A 341 SITE 4 AC1 14 HOH A 344 HOH A 357 CRYST1 50.377 50.377 146.167 90.00 90.00 90.00 P 41 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 0.019850 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006841 0.00000