HEADER HYDROLASE 01-MAR-16 5IJA TITLE [NIFE] HYDROGENASE MATURATION PROTEASE HYBD FROM THERMOCOCCUS TITLE 2 KODAKARENSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROGENASE-SPECIFIC MATURATION ENDOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS (STRAIN ATCC BAA-918 SOURCE 3 / JCM 12380 / KOD1); SOURCE 4 ORGANISM_TAXID: 69014; SOURCE 5 STRAIN: ATCC BAA-918 / JCM 12380 / KOD1; SOURCE 6 GENE: FRXA, TK2066; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROGENASE MATURATION PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KWON,Y.NISHITANI,S.WATANABE,K.MIKI REVDAT 4 08-NOV-23 5IJA 1 REMARK REVDAT 3 18-OCT-17 5IJA 1 JRNL REMARK REVDAT 2 14-SEP-16 5IJA 1 JRNL REVDAT 1 01-JUN-16 5IJA 0 JRNL AUTH S.KWON,Y.NISHITANI,S.WATANABE,Y.HIRAO,T.IMANAKA,T.KANAI, JRNL AUTH 2 H.ATOMI,K.MIKI JRNL TITL CRYSTAL STRUCTURE OF A [NIFE] HYDROGENASE MATURATION JRNL TITL 2 PROTEASE HYBD FROM THERMOCOCCUS KODAKARENSIS KOD1 JRNL REF PROTEINS V. 84 1321 2016 JRNL REFN ESSN 1097-0134 JRNL PMID 27192667 JRNL DOI 10.1002/PROT.25070 REMARK 2 REMARK 2 RESOLUTION. 1.82 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 27382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1381 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 41.1588 - 3.9077 0.98 2768 137 0.1743 0.2080 REMARK 3 2 3.9077 - 3.1020 0.99 2628 163 0.2038 0.2545 REMARK 3 3 3.1020 - 2.7099 0.99 2633 149 0.2492 0.2998 REMARK 3 4 2.7099 - 2.4622 0.99 2599 155 0.2512 0.2943 REMARK 3 5 2.4622 - 2.2857 0.99 2576 153 0.2430 0.3123 REMARK 3 6 2.2857 - 2.1510 0.99 2617 115 0.2547 0.2955 REMARK 3 7 2.1510 - 2.0433 0.99 2602 125 0.2722 0.3159 REMARK 3 8 2.0433 - 1.9543 1.00 2594 118 0.2879 0.3696 REMARK 3 9 1.9543 - 1.8791 1.00 2584 139 0.2908 0.4052 REMARK 3 10 1.8791 - 1.8142 0.93 2400 127 0.2945 0.3381 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.660 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 : 0.008 2247 REMARK 3 ANGLE : 1.020 3014 REMARK 3 CHIRALITY : 0.048 355 REMARK 3 PLANARITY : 0.004 386 REMARK 3 DIHEDRAL : 13.948 834 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 5IJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 9.0 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27433 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 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: 1CFZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, BIS-TRIS PROPANE, PH 9.0, REMARK 280 VAPOR DIFFUSION, 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 21.60450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.45300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.23350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.45300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.60450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.23350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 LYS A 65 CG CD CE NZ REMARK 470 GLU A 75 CG CD OE1 OE2 REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 ARG A 109 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 ILE A 122 CG1 CG2 CD1 REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 LYS B 65 CG CD CE NZ REMARK 470 GLU B 79 CG CD OE1 OE2 REMARK 470 LYS B 80 CG CD CE NZ REMARK 470 LEU B 81 CG CD1 CD2 REMARK 470 ILE B 85 CG1 CG2 CD1 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 LYS B 138 CG CD CE NZ REMARK 470 GLU B 141 CG CD OE1 OE2 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 LYS A 14 -110.92 62.70 REMARK 500 ALA A 83 -58.67 -121.17 REMARK 500 ILE A 122 42.77 -102.45 REMARK 500 LYS B 14 -117.47 50.86 REMARK 500 ASN B 48 37.32 -141.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 5IJA A 1 148 UNP Q8NKS1 Q8NKS1_THEKO 1 148 DBREF 5IJA B 1 148 UNP Q8NKS1 Q8NKS1_THEKO 1 148 SEQRES 1 A 148 MET ARG VAL LEU ILE LEU ALA LEU GLY ASN GLU LEU MET SEQRES 2 A 148 LYS ASP ASP GLY ALA GLY LEU LYS ALA GLY ARG ILE LEU SEQRES 3 A 148 ALA GLU LYS GLY TYR ASN VAL LEU GLU VAL GLY THR ASP SEQRES 4 A 148 ILE PHE ARG LEU ALA ASN HIS TYR ASN GLY GLU GLU ARG SEQRES 5 A 148 ILE VAL ILE ILE ASP ALA ILE LEU SER ASP LYS LEU LYS SEQRES 6 A 148 PRO GLY GLU VAL VAL HIS PHE SER GLY GLU GLU ILE PHE SEQRES 7 A 148 GLU LYS LEU LYS ALA GLU ILE ARG SER ALA HIS PHE MET SEQRES 8 A 148 GLY ALA ILE ASP GLY LEU LYS LEU LEU MET ALA LEU ASP SEQRES 9 A 148 GLU ARG LEU LYS ARG ALA GLU ILE HIS PHE ILE GLY ILE SEQRES 10 A 148 VAL ALA LYS GLU ILE ASP LEU GLY MET GLU LEU SER ASP SEQRES 11 A 148 GLU VAL LYS ALA GLY VAL GLN LYS ALA VAL GLU ILE ALA SEQRES 12 A 148 GLU LYS LEU ALA LYS SEQRES 1 B 148 MET ARG VAL LEU ILE LEU ALA LEU GLY ASN GLU LEU MET SEQRES 2 B 148 LYS ASP ASP GLY ALA GLY LEU LYS ALA GLY ARG ILE LEU SEQRES 3 B 148 ALA GLU LYS GLY TYR ASN VAL LEU GLU VAL GLY THR ASP SEQRES 4 B 148 ILE PHE ARG LEU ALA ASN HIS TYR ASN GLY GLU GLU ARG SEQRES 5 B 148 ILE VAL ILE ILE ASP ALA ILE LEU SER ASP LYS LEU LYS SEQRES 6 B 148 PRO GLY GLU VAL VAL HIS PHE SER GLY GLU GLU ILE PHE SEQRES 7 B 148 GLU LYS LEU LYS ALA GLU ILE ARG SER ALA HIS PHE MET SEQRES 8 B 148 GLY ALA ILE ASP GLY LEU LYS LEU LEU MET ALA LEU ASP SEQRES 9 B 148 GLU ARG LEU LYS ARG ALA GLU ILE HIS PHE ILE GLY ILE SEQRES 10 B 148 VAL ALA LYS GLU ILE ASP LEU GLY MET GLU LEU SER ASP SEQRES 11 B 148 GLU VAL LYS ALA GLY VAL GLN LYS ALA VAL GLU ILE ALA SEQRES 12 B 148 GLU LYS LEU ALA LYS FORMUL 3 HOH *125(H2 O) HELIX 1 AA1 ASN A 10 ASP A 16 5 7 HELIX 2 AA2 GLY A 17 LYS A 29 1 13 HELIX 3 AA3 ASP A 39 ALA A 44 5 6 HELIX 4 AA4 GLU A 75 LEU A 81 1 7 HELIX 5 AA5 SER A 87 ASP A 104 1 18 HELIX 6 AA6 ASP A 104 ALA A 110 1 7 HELIX 7 AA7 SER A 129 ALA A 147 1 19 HELIX 8 AA8 MET B 13 ASP B 16 5 4 HELIX 9 AA9 GLY B 17 LYS B 29 1 13 HELIX 10 AB1 PHE B 41 TYR B 47 1 7 HELIX 11 AB2 GLY B 74 GLU B 84 1 11 HELIX 12 AB3 PHE B 90 GLY B 92 5 3 HELIX 13 AB4 ALA B 93 ASP B 104 1 12 HELIX 14 AB5 ASP B 104 ARG B 109 1 6 HELIX 15 AB6 SER B 129 LYS B 148 1 20 SHEET 1 AA1 5 VAL A 33 GLY A 37 0 SHEET 2 AA1 5 VAL A 3 LEU A 8 1 N ILE A 5 O LEU A 34 SHEET 3 AA1 5 ARG A 52 ILE A 59 1 O VAL A 54 N LEU A 4 SHEET 4 AA1 5 GLU A 111 VAL A 118 1 O HIS A 113 N ILE A 55 SHEET 5 AA1 5 VAL A 69 SER A 73 -1 N PHE A 72 O PHE A 114 SHEET 1 AA2 5 VAL B 33 GLY B 37 0 SHEET 2 AA2 5 VAL B 3 LEU B 8 1 N ILE B 5 O LEU B 34 SHEET 3 AA2 5 ARG B 52 LEU B 60 1 O VAL B 54 N LEU B 6 SHEET 4 AA2 5 GLU B 111 VAL B 118 1 O ILE B 115 N ILE B 55 SHEET 5 AA2 5 VAL B 69 SER B 73 -1 N VAL B 70 O GLY B 116 SHEET 1 AA3 4 VAL B 33 GLY B 37 0 SHEET 2 AA3 4 VAL B 3 LEU B 8 1 N ILE B 5 O LEU B 34 SHEET 3 AA3 4 ARG B 52 LEU B 60 1 O VAL B 54 N LEU B 6 SHEET 4 AA3 4 ARG B 86 SER B 87 -1 O ARG B 86 N LEU B 60 CRYST1 43.209 64.467 106.906 90.00 90.00 90.00 P 21 21 21 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 0.023143 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009354 0.00000