HEADER HYDROLASE 19-OCT-07 3B2Y TITLE CRYSTAL STRUCTURE OF A PUTATIVE METALLOPEPTIDASE (SDEN_2526) FROM TITLE 2 SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLOPEPTIDASE CONTAINING CO-CATALYTIC METALLOACTIVE COMPND 3 SITE; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA DENITRIFICANS OS217; SOURCE 3 ORGANISM_TAXID: 318161; SOURCE 4 STRAIN: OS217, DSM 15013; SOURCE 5 ATCC: BAA-1090; SOURCE 6 GENE: YP_563529.1, SDEN_2526; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS METALLOPEPTIDASE CONTAINING CO-CATALYTIC METALLOACTIVE SITE, KEYWDS 2 STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 7 25-JAN-23 3B2Y 1 REMARK SEQADV LINK REVDAT 6 24-JUL-19 3B2Y 1 REMARK LINK REVDAT 5 25-OCT-17 3B2Y 1 REMARK REVDAT 4 13-JUL-11 3B2Y 1 VERSN REVDAT 3 28-JUL-10 3B2Y 1 TITLE KEYWDS REVDAT 2 24-FEB-09 3B2Y 1 VERSN REVDAT 1 27-NOV-07 3B2Y 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF METALLOPEPTIDASE CONTAINING JRNL TITL 2 CO-CATALYTIC METALLOACTIVE SITE (YP_563529.1) FROM JRNL TITL 3 SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 46725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2353 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3308 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 164 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4016 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : -1.84000 REMARK 3 B33 (A**2) : 2.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.121 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.986 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4194 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2796 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5695 ; 1.669 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6784 ; 1.143 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 536 ; 6.263 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;34.160 ;23.930 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 638 ;13.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.357 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 617 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4832 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 920 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 841 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2857 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2071 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2179 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 209 ; 0.177 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.096 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 7 ; 0.174 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.232 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.162 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2740 ; 2.651 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1081 ; 0.764 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4228 ; 3.614 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1648 ; 6.017 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1467 ; 8.064 ;11.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 273 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9855 27.1546 36.7775 REMARK 3 T TENSOR REMARK 3 T11: -0.1242 T22: -0.1156 REMARK 3 T33: -0.1081 T12: -0.0149 REMARK 3 T13: -0.0297 T23: 0.0538 REMARK 3 L TENSOR REMARK 3 L11: 1.2685 L22: 2.6326 REMARK 3 L33: 1.2962 L12: 0.1570 REMARK 3 L13: 0.1514 L23: -0.5527 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: -0.0796 S13: -0.0681 REMARK 3 S21: 0.1734 S22: -0.1102 S23: -0.3162 REMARK 3 S31: 0.1034 S32: 0.0060 S33: 0.1200 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 273 REMARK 3 ORIGIN FOR THE GROUP (A): 17.4489 56.6579 63.5149 REMARK 3 T TENSOR REMARK 3 T11: -0.1018 T22: -0.1053 REMARK 3 T33: -0.1449 T12: 0.0347 REMARK 3 T13: 0.0370 T23: 0.0385 REMARK 3 L TENSOR REMARK 3 L11: 1.7020 L22: 2.4713 REMARK 3 L33: 0.6588 L12: 0.0524 REMARK 3 L13: -0.2729 L23: -0.1055 REMARK 3 S TENSOR REMARK 3 S11: 0.0638 S12: 0.0462 S13: 0.0440 REMARK 3 S21: -0.2563 S22: -0.0825 S23: -0.2418 REMARK 3 S31: -0.0902 S32: -0.0924 S33: 0.0187 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. REMARK 3 4. TWO NICKEL IONS IDENTIFIED BY X-RAY FLUORESCENCE AND ANOMALOUS REMARK 3 DIFFERENCE FOURIERS ARE MODELED IN THE STRUCTURE. REMARK 3 5. RESIDUES FROM 133 TO 141, 208 TO 209 IN SUBUNIT A AND RESIDUES REMARK 3 FROM 60 TO 61, 132 TO 140 IN SUBUNIT B ARE DISORDERED AND NOT REMARK 3 MODELED IN THIS STRUCTURE. REMARK 4 REMARK 4 3B2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000045012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.07 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794, 1.0000, 0.9797 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : KOHZU, DOUBLE CRYSTAL SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46761 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 28.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : 0.38000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NANODROP, 20.4% PEG 6000, 0.1M MES PH REMARK 280 6.07, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 63.78850 REMARK 290 SMTRY3 2 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 300 REMARK: SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING REMARK 300 SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT REMARK 300 OLIGOMERIZATION STATE IN SOLUTION. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 0 REMARK 465 GLU A 133 REMARK 465 ASN A 134 REMARK 465 GLY A 135 REMARK 465 LYS A 136 REMARK 465 PRO A 137 REMARK 465 THR A 138 REMARK 465 PRO A 139 REMARK 465 ASN A 140 REMARK 465 GLU A 141 REMARK 465 ASP A 208 REMARK 465 GLY A 209 REMARK 465 LEU A 274 REMARK 465 GLY B 0 REMARK 465 SER B 60 REMARK 465 GLN B 61 REMARK 465 LEU B 132 REMARK 465 GLU B 133 REMARK 465 ASN B 134 REMARK 465 GLY B 135 REMARK 465 LYS B 136 REMARK 465 PRO B 137 REMARK 465 THR B 138 REMARK 465 PRO B 139 REMARK 465 ASN B 140 REMARK 465 LEU B 274 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 15 CD OE1 OE2 REMARK 470 GLN A 30 CD OE1 NE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 ARG A 162 CD NE CZ NH1 NH2 REMARK 470 ARG A 190 CD NE CZ NH1 NH2 REMARK 470 LYS A 204 CD CE NZ REMARK 470 LYS A 207 CE NZ REMARK 470 ILE A 211 CG1 CG2 CD1 REMARK 470 ASP A 212 CG OD1 OD2 REMARK 470 THR B 2 OG1 CG2 REMARK 470 GLU B 15 CD OE1 OE2 REMARK 470 LYS B 41 CE NZ REMARK 470 ARG B 62 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 128 NE CZ NH1 NH2 REMARK 470 THR B 131 OG1 CG2 REMARK 470 GLU B 141 CG CD OE1 OE2 REMARK 470 GLN B 155 CD OE1 NE2 REMARK 470 ARG B 162 CD NE CZ NH1 NH2 REMARK 470 LYS B 207 CG CD CE NZ REMARK 470 ASP B 208 CG OD1 OD2 REMARK 470 ASP B 212 CG OD1 OD2 REMARK 470 ASP B 218 CG OD1 OD2 REMARK 470 ILE B 273 CG1 CG2 CD1 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 310 O HOH A 332 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 207 C LYS A 207 O 0.167 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 78 52.85 -94.84 REMARK 500 THR A 131 -10.12 -151.32 REMARK 500 GLU A 213 -0.92 71.61 REMARK 500 ASP A 226 -154.11 -144.84 REMARK 500 GLU B 78 55.35 -101.56 REMARK 500 PRO B 184 38.66 -81.20 REMARK 500 ASP B 208 33.54 -150.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 275 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 75 ND1 REMARK 620 2 GLU A 78 OE1 105.4 REMARK 620 3 GLU A 78 OE2 91.4 62.7 REMARK 620 4 HIS A 169 ND1 102.0 86.9 149.1 REMARK 620 5 HOH A 310 O 143.6 98.8 76.0 106.1 REMARK 620 6 HOH A 332 O 89.9 160.9 106.4 101.3 62.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 275 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 75 ND1 REMARK 620 2 GLU B 78 OE1 102.0 REMARK 620 3 GLU B 78 OE2 89.4 60.1 REMARK 620 4 HIS B 169 ND1 101.1 91.2 151.1 REMARK 620 5 HOH B 293 O 148.4 94.9 76.0 105.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 275 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 275 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 375165 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3B2Y A 1 274 UNP Q12L70 Q12L70_SHEDO 1 274 DBREF 3B2Y B 1 274 UNP Q12L70 Q12L70_SHEDO 1 274 SEQADV 3B2Y GLY A 0 UNP Q12L70 EXPRESSION TAG SEQADV 3B2Y GLY B 0 UNP Q12L70 EXPRESSION TAG SEQRES 1 A 275 GLY MSE THR SER ARG SER PRO PHE GLU SER PHE VAL TRP SEQRES 2 A 275 GLN SER GLU ILE PHE ASN CYS GLN SER ASN ASP ILE ASP SEQRES 3 A 275 ALA PHE TYR ALA GLN LEU ALA GLU GLU VAL ASN ARG LEU SEQRES 4 A 275 GLY LEU LYS LYS ASN THR LEU GLY SER VAL ASP SER PHE SEQRES 5 A 275 ALA ILE ASN LEU TYR GLN SER ALA SER GLN ARG SER ASP SEQRES 6 A 275 LEU PRO SER LEU LEU ILE SER SER GLY PHE HIS GLY GLU SEQRES 7 A 275 GLU ALA ALA GLY PRO TRP GLY MSE LEU HIS PHE LEU ARG SEQRES 8 A 275 GLY LEU GLN PRO ALA LEU PHE GLU ARG VAL ASN LEU SER SEQRES 9 A 275 LEU LEU PRO LEU VAL ASN PRO THR GLY PHE LYS ALA GLY SEQRES 10 A 275 HIS ARG PHE ASN ARG PHE GLY GLU ASN PRO ASN ARG GLY SEQRES 11 A 275 PHE THR LEU GLU ASN GLY LYS PRO THR PRO ASN GLU HIS SEQRES 12 A 275 THR SER LEU GLU GLY LYS LEU LEU LEU GLU HIS ALA GLN SEQRES 13 A 275 LEU LEU CYS ALA ALA SER ARG ASP GLY ILE LEU THR CYS SEQRES 14 A 275 HIS GLU ASP VAL LEU MSE ASN GLU THR TYR VAL TYR SER SEQRES 15 A 275 PHE GLU PRO THR GLN THR PRO GLY ARG PHE SER LEU GLY SEQRES 16 A 275 LEU ARG ASP ALA LEU GLY GLN TYR PHE LYS LEU ALA LYS SEQRES 17 A 275 ASP GLY PHE ILE ASP GLU CYS PRO VAL THR ASP GLY VAL SEQRES 18 A 275 ILE PHE ASN HIS PHE ASP THR SER PHE GLU ALA PHE LEU SEQRES 19 A 275 VAL ARG SER GLY ALA LYS LEU ALA ALA CYS SER GLU THR SEQRES 20 A 275 PRO GLY GLN GLU ASP PHE ASP ARG ARG VAL GLN ALA ASN SEQRES 21 A 275 SER ALA ALA MSE GLY GLN PHE ILE ALA HIS CYS ALA PRO SEQRES 22 A 275 ILE LEU SEQRES 1 B 275 GLY MSE THR SER ARG SER PRO PHE GLU SER PHE VAL TRP SEQRES 2 B 275 GLN SER GLU ILE PHE ASN CYS GLN SER ASN ASP ILE ASP SEQRES 3 B 275 ALA PHE TYR ALA GLN LEU ALA GLU GLU VAL ASN ARG LEU SEQRES 4 B 275 GLY LEU LYS LYS ASN THR LEU GLY SER VAL ASP SER PHE SEQRES 5 B 275 ALA ILE ASN LEU TYR GLN SER ALA SER GLN ARG SER ASP SEQRES 6 B 275 LEU PRO SER LEU LEU ILE SER SER GLY PHE HIS GLY GLU SEQRES 7 B 275 GLU ALA ALA GLY PRO TRP GLY MSE LEU HIS PHE LEU ARG SEQRES 8 B 275 GLY LEU GLN PRO ALA LEU PHE GLU ARG VAL ASN LEU SER SEQRES 9 B 275 LEU LEU PRO LEU VAL ASN PRO THR GLY PHE LYS ALA GLY SEQRES 10 B 275 HIS ARG PHE ASN ARG PHE GLY GLU ASN PRO ASN ARG GLY SEQRES 11 B 275 PHE THR LEU GLU ASN GLY LYS PRO THR PRO ASN GLU HIS SEQRES 12 B 275 THR SER LEU GLU GLY LYS LEU LEU LEU GLU HIS ALA GLN SEQRES 13 B 275 LEU LEU CYS ALA ALA SER ARG ASP GLY ILE LEU THR CYS SEQRES 14 B 275 HIS GLU ASP VAL LEU MSE ASN GLU THR TYR VAL TYR SER SEQRES 15 B 275 PHE GLU PRO THR GLN THR PRO GLY ARG PHE SER LEU GLY SEQRES 16 B 275 LEU ARG ASP ALA LEU GLY GLN TYR PHE LYS LEU ALA LYS SEQRES 17 B 275 ASP GLY PHE ILE ASP GLU CYS PRO VAL THR ASP GLY VAL SEQRES 18 B 275 ILE PHE ASN HIS PHE ASP THR SER PHE GLU ALA PHE LEU SEQRES 19 B 275 VAL ARG SER GLY ALA LYS LEU ALA ALA CYS SER GLU THR SEQRES 20 B 275 PRO GLY GLN GLU ASP PHE ASP ARG ARG VAL GLN ALA ASN SEQRES 21 B 275 SER ALA ALA MSE GLY GLN PHE ILE ALA HIS CYS ALA PRO SEQRES 22 B 275 ILE LEU MODRES 3B2Y MSE A 1 MET SELENOMETHIONINE MODRES 3B2Y MSE A 85 MET SELENOMETHIONINE MODRES 3B2Y MSE A 174 MET SELENOMETHIONINE MODRES 3B2Y MSE A 263 MET SELENOMETHIONINE MODRES 3B2Y MSE B 1 MET SELENOMETHIONINE MODRES 3B2Y MSE B 85 MET SELENOMETHIONINE MODRES 3B2Y MSE B 174 MET SELENOMETHIONINE MODRES 3B2Y MSE B 263 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 85 8 HET MSE A 174 8 HET MSE A 263 8 HET MSE B 1 8 HET MSE B 85 8 HET MSE B 174 8 HET MSE B 263 8 HET NI A 275 1 HET NI B 275 1 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *230(H2 O) HELIX 1 1 ASP A 23 GLY A 39 1 17 HELIX 2 2 ALA A 80 LEU A 92 1 13 HELIX 3 3 GLN A 93 ARG A 99 5 7 HELIX 4 4 ASN A 109 ALA A 115 1 7 HELIX 5 5 SER A 144 GLU A 152 1 9 HELIX 6 6 HIS A 153 SER A 161 1 9 HELIX 7 7 GLY A 189 GLN A 201 1 13 HELIX 8 8 SER A 228 SER A 236 1 9 HELIX 9 9 ASP A 251 ALA A 271 1 21 HELIX 10 10 ASP B 23 GLY B 39 1 17 HELIX 11 11 ALA B 80 GLY B 91 1 12 HELIX 12 12 LEU B 92 ARG B 99 5 8 HELIX 13 13 ASN B 109 GLY B 116 1 8 HELIX 14 14 SER B 144 GLU B 152 1 9 HELIX 15 15 HIS B 153 SER B 161 1 9 HELIX 16 16 GLY B 189 GLN B 201 1 13 HELIX 17 17 SER B 228 SER B 236 1 9 HELIX 18 18 ASP B 251 ALA B 271 1 21 SHEET 1 A 2 GLN A 13 SER A 14 0 SHEET 2 A 2 CYS A 19 GLN A 20 -1 O CYS A 19 N SER A 14 SHEET 1 B 2 LYS A 42 VAL A 48 0 SHEET 2 B 2 PHE A 51 GLN A 57 -1 O ILE A 53 N GLY A 46 SHEET 1 C 6 ASN A 101 LEU A 105 0 SHEET 2 C 6 SER A 67 SER A 72 1 N LEU A 69 O SER A 103 SHEET 3 C 6 GLY A 164 ASP A 171 1 O LEU A 166 N LEU A 69 SHEET 4 C 6 ALA A 242 PRO A 247 1 O THR A 246 N ASP A 171 SHEET 5 C 6 TYR A 178 PHE A 182 -1 N TYR A 180 O CYS A 243 SHEET 6 C 6 VAL A 220 PHE A 222 1 O ILE A 221 N SER A 181 SHEET 1 D 2 GLN B 13 SER B 14 0 SHEET 2 D 2 CYS B 19 GLN B 20 -1 O CYS B 19 N SER B 14 SHEET 1 E 8 LYS B 42 VAL B 48 0 SHEET 2 E 8 PHE B 51 GLN B 57 -1 O ILE B 53 N GLY B 46 SHEET 3 E 8 ASN B 101 LEU B 105 -1 O LEU B 105 N TYR B 56 SHEET 4 E 8 SER B 67 SER B 72 1 N LEU B 69 O SER B 103 SHEET 5 E 8 GLY B 164 ASP B 171 1 O CYS B 168 N SER B 72 SHEET 6 E 8 ALA B 242 PRO B 247 1 O SER B 244 N HIS B 169 SHEET 7 E 8 TYR B 178 PHE B 182 -1 N TYR B 180 O CYS B 243 SHEET 8 E 8 VAL B 220 PHE B 222 1 O ILE B 221 N VAL B 179 SHEET 1 F 2 PHE B 210 ILE B 211 0 SHEET 2 F 2 CYS B 214 PRO B 215 -1 O CYS B 214 N ILE B 211 LINK C MSE A 1 N THR A 2 1555 1555 1.33 LINK C GLY A 84 N MSE A 85 1555 1555 1.33 LINK C MSE A 85 N LEU A 86 1555 1555 1.32 LINK C LEU A 173 N MSE A 174 1555 1555 1.33 LINK C MSE A 174 N ASN A 175 1555 1555 1.34 LINK C ALA A 262 N MSE A 263 1555 1555 1.33 LINK C MSE A 263 N GLY A 264 1555 1555 1.33 LINK C MSE B 1 N THR B 2 1555 1555 1.33 LINK C GLY B 84 N MSE B 85 1555 1555 1.34 LINK C MSE B 85 N LEU B 86 1555 1555 1.32 LINK C LEU B 173 N MSE B 174 1555 1555 1.33 LINK C MSE B 174 N ASN B 175 1555 1555 1.33 LINK C ALA B 262 N MSE B 263 1555 1555 1.31 LINK C MSE B 263 N GLY B 264 1555 1555 1.34 LINK ND1 HIS A 75 NI NI A 275 1555 1555 2.22 LINK OE1 GLU A 78 NI NI A 275 1555 1555 2.09 LINK OE2 GLU A 78 NI NI A 275 1555 1555 2.21 LINK ND1 HIS A 169 NI NI A 275 1555 1555 2.24 LINK NI NI A 275 O HOH A 310 1555 1555 2.30 LINK NI NI A 275 O HOH A 332 1555 1555 1.81 LINK ND1 HIS B 75 NI NI B 275 1555 1555 2.25 LINK OE1 GLU B 78 NI NI B 275 1555 1555 2.08 LINK OE2 GLU B 78 NI NI B 275 1555 1555 2.32 LINK ND1 HIS B 169 NI NI B 275 1555 1555 2.15 LINK NI NI B 275 O HOH B 293 1555 1555 2.38 SITE 1 AC1 5 HIS A 75 GLU A 78 HIS A 169 HOH A 310 SITE 2 AC1 5 HOH A 332 SITE 1 AC2 4 HIS B 75 GLU B 78 HIS B 169 HOH B 293 CRYST1 43.715 127.577 49.303 90.00 116.28 90.00 P 1 21 1 4 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 0.022875 0.000000 0.011294 0.00000 SCALE2 0.000000 0.007838 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022620 0.00000 HETATM 1 N MSE A 1 25.832 48.184 52.261 1.00 44.09 N HETATM 2 CA MSE A 1 26.292 48.621 50.899 1.00 46.24 C HETATM 3 C MSE A 1 27.525 47.849 50.390 1.00 46.56 C HETATM 4 O MSE A 1 28.491 47.633 51.122 1.00 43.99 O HETATM 5 CB MSE A 1 26.582 50.124 50.891 1.00 45.51 C HETATM 6 CG MSE A 1 27.360 50.614 49.666 1.00 47.02 C HETATM 7 SE MSE A 1 26.956 52.478 49.193 0.75 51.13 SE HETATM 8 CE MSE A 1 25.199 52.163 48.422 1.00 35.39 C