HEADER HYDROLASE 25-NOV-15 5EYH TITLE CRYSTAL STRUCTURE OF IMPASE/NADP PHOSPHATASE COMPLEXED WITH NADP AND TITLE 2 CA2+ AT PH 7.0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSITOL MONOPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IMPASE/NADP PHOSPHATASE, MYO-INOSITOL-1(OR 4)- COMPND 5 MONOPHOSPHATASE; COMPND 6 EC: 3.1.3.25; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS IMPASE, FIG SUPERFAMILY, SUBSTRATE BOUND COMPLEX, PHOSPHATASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BHATTACHARYYA,D.DUTTA,A.K.GHOSH,A.K.DAS REVDAT 3 20-MAR-24 5EYH 1 LINK REVDAT 2 25-JAN-17 5EYH 1 JRNL REVDAT 1 23-DEC-15 5EYH 0 SPRSDE 23-DEC-15 5EYH 4G64 JRNL AUTH S.BHATTACHARYYA,A.DUTTA,D.DUTTA,A.K.GHOSH,A.K.DAS JRNL TITL STRUCTURAL ELUCIDATION OF THE NADP(H) PHOSPHATASE ACTIVITY JRNL TITL 2 OF STAPHYLOCOCCAL DUAL-SPECIFIC IMPASE/NADP(H) PHOSPHATASE JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 281 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 26894675 JRNL DOI 10.1107/S2059798316000620 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 19318 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1387 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4125 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 113 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.12000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.803 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.296 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.108 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4403 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4136 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5984 ; 1.842 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9537 ; 1.068 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 523 ; 7.655 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;40.017 ;25.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 761 ;17.026 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.746 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4881 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1002 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2083 ; 2.854 ; 3.734 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2082 ; 2.850 ; 3.734 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2600 ; 4.380 ; 5.588 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 263 B 4 263 15697 0.090 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5EYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215711. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20372 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.499 REMARK 200 RESOLUTION RANGE LOW (A) : 75.905 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48500 REMARK 200 R SYM FOR SHELL (I) : 0.48500 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 10.2.35, MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CACL2 2H2O, 0.1M HEPES PH 7.0, REMARK 280 15% (W/V) PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K 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 30.16550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 TYR A 264 REMARK 465 ARG A 265 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 HIS B 38 REMARK 465 ARG B 39 REMARK 465 PHE B 40 REMARK 465 ASP B 41 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 39 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 52 CD OE1 NE2 REMARK 470 TYR A 61 OH REMARK 470 GLN A 170 NE2 REMARK 470 LYS A 206 NZ REMARK 470 GLN B 7 CD OE1 NE2 REMARK 470 GLN B 19 CD OE1 NE2 REMARK 470 LYS B 36 CB CG CD CE NZ REMARK 470 ARG B 37 CD NE CZ NH1 NH2 REMARK 470 LEU B 42 CD1 CD2 REMARK 470 TYR B 61 OH REMARK 470 ASN B 79 CG OD1 ND2 REMARK 470 GLU B 135 CD OE1 OE2 REMARK 470 PHE B 142 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 ARG B 265 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 B 412 O HOH B 446 1.96 REMARK 500 O PRO B 115 NH1 ARG B 133 2.13 REMARK 500 O PRO A 115 NH1 ARG A 133 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ILE A 157 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 ILE B 157 CB - CA - C ANGL. DEV. = -12.3 DEGREES 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 LYS A 36 -86.72 -117.15 REMARK 500 HIS A 38 -172.05 -176.18 REMARK 500 GLU A 71 30.57 -97.38 REMARK 500 GLU A 80 60.87 -117.23 REMARK 500 ASN A 204 59.78 -156.37 REMARK 500 LYS B 36 -70.23 -103.28 REMARK 500 GLU B 71 32.48 -98.50 REMARK 500 GLU B 80 58.20 -115.23 REMARK 500 ASN B 204 61.43 -156.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 237 ALA A 238 145.25 REMARK 500 GLY B 237 ALA B 238 145.24 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 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE2 REMARK 620 2 ASP A 88 OD1 99.1 REMARK 620 3 ASP A 88 OD2 97.4 46.5 REMARK 620 4 ILE A 90 O 160.6 75.3 92.0 REMARK 620 5 NAP A 306 O3X 101.0 112.4 67.3 98.3 REMARK 620 6 NAP A 306 O3X 109.7 111.1 68.3 89.5 8.8 REMARK 620 7 HOH A 406 O 83.9 89.6 135.9 77.5 156.0 152.1 REMARK 620 8 HOH A 408 O 83.9 166.1 146.9 97.4 80.0 80.1 77.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 70 OE1 REMARK 620 2 NAP A 306 O1X 108.0 REMARK 620 3 NAP A 306 O1X 102.4 6.6 REMARK 620 4 HOH A 408 O 98.2 82.8 80.0 REMARK 620 5 HOH A 409 O 79.6 140.9 137.6 58.1 REMARK 620 6 HOH A 422 O 109.4 133.8 140.3 117.0 72.6 REMARK 620 7 HOH A 426 O 173.7 67.0 72.3 77.6 101.8 76.8 REMARK 620 8 HOH A 459 O 87.1 77.0 79.8 159.8 142.0 78.8 95.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 88 OD2 REMARK 620 2 ASP A 91 OD1 106.3 REMARK 620 3 ASP A 209 OD1 117.0 111.4 REMARK 620 4 NAP A 306 O3X 84.5 104.8 128.7 REMARK 620 5 NAP A 306 O3X 85.6 95.5 136.0 9.4 REMARK 620 6 NAP A 306 O2B 147.7 83.5 85.8 63.2 62.5 REMARK 620 7 NAP A 306 O2B 144.4 83.8 88.8 60.0 59.2 3.4 REMARK 620 8 HOH A 414 O 107.3 145.3 59.0 70.4 78.8 63.4 63.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 70 OE1 REMARK 620 2 ASP B 88 OD1 106.7 REMARK 620 3 ASP B 88 OD2 95.5 46.0 REMARK 620 4 ILE B 90 O 171.8 77.3 92.4 REMARK 620 5 NAP B 303 O2X 91.1 113.7 69.6 93.7 REMARK 620 6 HOH B 418 O 91.5 88.3 133.8 81.4 156.0 REMARK 620 7 HOH B 423 O 74.1 171.4 142.5 100.8 74.7 83.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 88 OD2 REMARK 620 2 ASP B 91 OD1 96.4 REMARK 620 3 ASP B 209 OD1 117.8 102.7 REMARK 620 4 NAP B 303 O2B 142.4 80.2 99.3 REMARK 620 5 NAP B 303 O2X 85.7 95.4 147.9 57.8 REMARK 620 6 HOH B 439 O 102.5 159.2 76.1 79.6 77.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EYG RELATED DB: PDB DBREF1 5EYH A 1 265 UNP A0A0D6HL44_STAAU DBREF2 5EYH A A0A0D6HL44 1 265 DBREF1 5EYH B 1 265 UNP A0A0D6HL44_STAAU DBREF2 5EYH B A0A0D6HL44 1 265 SEQADV 5EYH PHE A 142 UNP A0A0D6HL4 ILE 142 ENGINEERED MUTATION SEQADV 5EYH PHE B 142 UNP A0A0D6HL4 ILE 142 ENGINEERED MUTATION SEQRES 1 A 265 MET THR ASP LYS THR LEU GLN GLN ILE ASP LYS LEU ILE SEQRES 2 A 265 CYS SER TRP LEU LYS GLN ILE ASP ASN VAL ILE PRO GLN SEQRES 3 A 265 LEU ILE MET GLU MET THR THR GLU THR LYS ARG HIS ARG SEQRES 4 A 265 PHE ASP LEU VAL THR ASN VAL ASP LYS GLN ILE GLN GLN SEQRES 5 A 265 GLN PHE GLN GLN PHE LEU ALA THR TYR PHE PRO GLU HIS SEQRES 6 A 265 GLN LEU LEU ALA GLU GLU LYS SER ASN ALA MET ILE THR SEQRES 7 A 265 ASN GLU ILE ASN HIS LEU TRP ILE MET ASP PRO ILE ASP SEQRES 8 A 265 GLY THR ALA ASN LEU VAL LYS GLN GLN GLU ASP TYR CYS SEQRES 9 A 265 ILE ILE LEU ALA TYR PHE TYR GLU GLY LYS PRO MET LEU SEQRES 10 A 265 SER TYR VAL TYR ASP TYR PRO HIS LYS LYS LEU TYR LYS SEQRES 11 A 265 ALA ILE ARG GLY GLU GLY ALA PHE CYS ASN GLY PHE LYS SEQRES 12 A 265 MET GLU GLU PRO PRO SER LEU LYS LEU GLU ASP ALA ILE SEQRES 13 A 265 ILE SER PHE ASN ALA GLN VAL MET ASN LEU ASP THR VAL SEQRES 14 A 265 GLN ASP LEU PHE ASP ALA SER PHE SER TYR ARG LEU VAL SEQRES 15 A 265 GLY ALA CYS GLY LEU ASP SER MET ARG VAL ALA LYS GLY SEQRES 16 A 265 GLN PHE GLY ALA HIS ILE ASN THR ASN PRO LYS PRO TRP SEQRES 17 A 265 ASP ILE ALA ALA GLN PHE LEU PHE ALA GLU LEU LEU ASN SEQRES 18 A 265 LEU LYS MET THR THR LEU ASP GLY LYS ALA ILE ASP HIS SEQRES 19 A 265 LEU LYS GLY ALA PRO PHE ILE ILE SER ASN LYS ALA CYS SEQRES 20 A 265 HIS GLU THR VAL LEU LYS ILE LEU ASN ALA ASN GLY GLY SEQRES 21 A 265 TYR GLN LYS TYR ARG SEQRES 1 B 265 MET THR ASP LYS THR LEU GLN GLN ILE ASP LYS LEU ILE SEQRES 2 B 265 CYS SER TRP LEU LYS GLN ILE ASP ASN VAL ILE PRO GLN SEQRES 3 B 265 LEU ILE MET GLU MET THR THR GLU THR LYS ARG HIS ARG SEQRES 4 B 265 PHE ASP LEU VAL THR ASN VAL ASP LYS GLN ILE GLN GLN SEQRES 5 B 265 GLN PHE GLN GLN PHE LEU ALA THR TYR PHE PRO GLU HIS SEQRES 6 B 265 GLN LEU LEU ALA GLU GLU LYS SER ASN ALA MET ILE THR SEQRES 7 B 265 ASN GLU ILE ASN HIS LEU TRP ILE MET ASP PRO ILE ASP SEQRES 8 B 265 GLY THR ALA ASN LEU VAL LYS GLN GLN GLU ASP TYR CYS SEQRES 9 B 265 ILE ILE LEU ALA TYR PHE TYR GLU GLY LYS PRO MET LEU SEQRES 10 B 265 SER TYR VAL TYR ASP TYR PRO HIS LYS LYS LEU TYR LYS SEQRES 11 B 265 ALA ILE ARG GLY GLU GLY ALA PHE CYS ASN GLY PHE LYS SEQRES 12 B 265 MET GLU GLU PRO PRO SER LEU LYS LEU GLU ASP ALA ILE SEQRES 13 B 265 ILE SER PHE ASN ALA GLN VAL MET ASN LEU ASP THR VAL SEQRES 14 B 265 GLN ASP LEU PHE ASP ALA SER PHE SER TYR ARG LEU VAL SEQRES 15 B 265 GLY ALA CYS GLY LEU ASP SER MET ARG VAL ALA LYS GLY SEQRES 16 B 265 GLN PHE GLY ALA HIS ILE ASN THR ASN PRO LYS PRO TRP SEQRES 17 B 265 ASP ILE ALA ALA GLN PHE LEU PHE ALA GLU LEU LEU ASN SEQRES 18 B 265 LEU LYS MET THR THR LEU ASP GLY LYS ALA ILE ASP HIS SEQRES 19 B 265 LEU LYS GLY ALA PRO PHE ILE ILE SER ASN LYS ALA CYS SEQRES 20 B 265 HIS GLU THR VAL LEU LYS ILE LEU ASN ALA ASN GLY GLY SEQRES 21 B 265 TYR GLN LYS TYR ARG HET CA A 301 1 HET CA A 302 1 HET GOL A 303 6 HET GOL A 304 6 HET CA A 305 1 HET NAP A 306 96 HET CA B 301 1 HET CA B 302 1 HET NAP B 303 48 HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 CA 5(CA 2+) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 8 NAP 2(C21 H28 N7 O17 P3) FORMUL 12 HOH *158(H2 O) HELIX 1 AA1 THR A 5 GLU A 30 1 26 HELIX 2 AA2 ASN A 45 PHE A 62 1 18 HELIX 3 AA3 GLY A 92 GLN A 100 1 9 HELIX 4 AA4 LYS A 151 ASP A 154 5 4 HELIX 5 AA5 ASN A 165 SER A 176 1 12 HELIX 6 AA6 ALA A 184 LYS A 194 1 11 HELIX 7 AA7 LYS A 206 ALA A 211 1 6 HELIX 8 AA8 ALA A 212 LEU A 220 1 9 HELIX 9 AA9 CYS A 247 ALA A 257 1 11 HELIX 10 AB1 THR B 5 GLU B 30 1 26 HELIX 11 AB2 ASN B 45 PHE B 62 1 18 HELIX 12 AB3 GLY B 92 GLN B 100 1 9 HELIX 13 AB4 LYS B 151 ASP B 154 5 4 HELIX 14 AB5 ASN B 165 SER B 176 1 12 HELIX 15 AB6 ALA B 184 LYS B 194 1 11 HELIX 16 AB7 LYS B 206 ALA B 211 1 6 HELIX 17 AB8 ALA B 212 LEU B 220 1 9 HELIX 18 AB9 CYS B 247 ALA B 257 1 11 SHEET 1 AA1 2 THR A 33 THR A 35 0 SHEET 2 AA1 2 LEU A 42 THR A 44 -1 O VAL A 43 N GLU A 34 SHEET 1 AA2 7 GLN A 66 ALA A 69 0 SHEET 2 AA2 7 HIS A 83 ASP A 91 1 O TRP A 85 N LEU A 68 SHEET 3 AA2 7 CYS A 104 TYR A 111 -1 O CYS A 104 N ASP A 91 SHEET 4 AA2 7 LYS A 114 ASP A 122 -1 O LEU A 117 N TYR A 109 SHEET 5 AA2 7 LYS A 127 ILE A 132 -1 O LYS A 127 N ASP A 122 SHEET 6 AA2 7 GLY A 136 CYS A 139 -1 O PHE A 138 N LYS A 130 SHEET 7 AA2 7 PHE A 142 MET A 144 -1 O PHE A 142 N CYS A 139 SHEET 1 AA3 5 SER A 178 TYR A 179 0 SHEET 2 AA3 5 ILE A 156 SER A 158 1 N ILE A 157 O SER A 178 SHEET 3 AA3 5 ALA A 199 ASN A 202 1 O ILE A 201 N SER A 158 SHEET 4 AA3 5 PHE A 240 SER A 243 -1 O PHE A 240 N ASN A 202 SHEET 5 AA3 5 LYS A 223 THR A 226 -1 N LYS A 223 O SER A 243 SHEET 1 AA4 2 THR B 33 GLU B 34 0 SHEET 2 AA4 2 VAL B 43 THR B 44 -1 O VAL B 43 N GLU B 34 SHEET 1 AA5 7 GLN B 66 ALA B 69 0 SHEET 2 AA5 7 HIS B 83 ASP B 91 1 O TRP B 85 N LEU B 68 SHEET 3 AA5 7 CYS B 104 TYR B 111 -1 O CYS B 104 N ASP B 91 SHEET 4 AA5 7 LYS B 114 ASP B 122 -1 O LEU B 117 N TYR B 109 SHEET 5 AA5 7 LYS B 127 ILE B 132 -1 O LYS B 127 N ASP B 122 SHEET 6 AA5 7 GLY B 136 CYS B 139 -1 O PHE B 138 N LYS B 130 SHEET 7 AA5 7 PHE B 142 MET B 144 -1 O MET B 144 N ALA B 137 SHEET 1 AA6 5 SER B 178 TYR B 179 0 SHEET 2 AA6 5 ILE B 156 SER B 158 1 N ILE B 157 O SER B 178 SHEET 3 AA6 5 ALA B 199 ASN B 202 1 O ILE B 201 N SER B 158 SHEET 4 AA6 5 PHE B 240 SER B 243 -1 O PHE B 240 N ASN B 202 SHEET 5 AA6 5 LYS B 223 THR B 226 -1 N LYS B 223 O SER B 243 LINK OE2 GLU A 70 CA CA A 301 1555 1555 2.10 LINK OE1 GLU A 70 CA CA A 302 1555 1555 2.33 LINK OD1 ASP A 88 CA CA A 301 1555 1555 2.26 LINK OD2 ASP A 88 CA CA A 301 1555 1555 2.95 LINK OD2 ASP A 88 CA CA A 305 1555 1555 2.22 LINK O ILE A 90 CA CA A 301 1555 1555 2.28 LINK OD1 ASP A 91 CA CA A 305 1555 1555 2.27 LINK OD1 ASP A 209 CA CA A 305 1555 1555 2.15 LINK CA CA A 301 O3XANAP A 306 1555 1555 2.23 LINK CA CA A 301 O3XBNAP A 306 1555 1555 2.32 LINK CA CA A 301 O HOH A 406 1555 1555 2.37 LINK CA CA A 301 O HOH A 408 1555 1555 2.38 LINK CA CA A 302 O1XANAP A 306 1555 1555 2.40 LINK CA CA A 302 O1XBNAP A 306 1555 1555 2.24 LINK CA CA A 302 O HOH A 408 1555 1555 2.41 LINK CA CA A 302 O HOH A 409 1555 1555 2.90 LINK CA CA A 302 O HOH A 422 1555 1555 2.29 LINK CA CA A 302 O HOH A 426 1555 1555 2.54 LINK CA CA A 302 O HOH A 459 1555 1555 2.29 LINK CA CA A 305 O3XANAP A 306 1555 1555 2.14 LINK CA CA A 305 O3XBNAP A 306 1555 1555 2.20 LINK CA CA A 305 O2BANAP A 306 1555 1555 2.45 LINK CA CA A 305 O2BBNAP A 306 1555 1555 2.57 LINK CA CA A 305 O HOH A 414 1555 1555 3.19 LINK OE1 GLU B 70 CA CA B 302 1555 1555 2.44 LINK OD2 ASP B 88 CA CA B 301 1555 1555 2.33 LINK OD1 ASP B 88 CA CA B 302 1555 1555 2.24 LINK OD2 ASP B 88 CA CA B 302 1555 1555 3.05 LINK O ILE B 90 CA CA B 302 1555 1555 2.40 LINK OD1 ASP B 91 CA CA B 301 1555 1555 2.54 LINK OD1 ASP B 209 CA CA B 301 1555 1555 2.05 LINK CA CA B 301 O2B NAP B 303 1555 1555 2.49 LINK CA CA B 301 O2X NAP B 303 1555 1555 2.28 LINK CA CA B 301 O HOH B 439 1555 1555 2.72 LINK CA CA B 302 O2X NAP B 303 1555 1555 2.37 LINK CA CA B 302 O HOH B 418 1555 1555 2.33 LINK CA CA B 302 O HOH B 423 1555 1555 2.11 SITE 1 AC1 6 GLU A 70 ASP A 88 ILE A 90 NAP A 306 SITE 2 AC1 6 HOH A 406 HOH A 408 SITE 1 AC2 7 GLU A 70 NAP A 306 HOH A 408 HOH A 409 SITE 2 AC2 7 HOH A 422 HOH A 426 HOH A 459 SITE 1 AC3 2 THR A 35 LYS A 36 SITE 1 AC4 7 PHE A 173 ASP A 174 SER A 176 PHE A 177 SITE 2 AC4 7 HOH A 451 GLN B 162 HOH B 407 SITE 1 AC5 4 ASP A 88 ASP A 91 ASP A 209 NAP A 306 SITE 1 AC6 37 HIS A 38 PHE A 40 GLU A 70 ASP A 88 SITE 2 AC6 37 ILE A 90 ASP A 91 GLY A 92 THR A 93 SITE 3 AC6 37 ALA A 94 ASN A 160 GLN A 162 VAL A 163 SITE 4 AC6 37 GLY A 183 ALA A 184 CYS A 185 ASN A 202 SITE 5 AC6 37 THR A 203 ASN A 204 ASP A 209 CA A 301 SITE 6 AC6 37 CA A 302 CA A 305 HOH A 401 HOH A 402 SITE 7 AC6 37 HOH A 405 HOH A 408 HOH A 414 HOH A 425 SITE 8 AC6 37 HOH A 426 HOH A 459 PHE B 173 ASP B 174 SITE 9 AC6 37 SER B 176 PHE B 177 SER B 178 ARG B 180 SITE 10 AC6 37 HOH B 415 SITE 1 AC7 5 ASP B 88 ASP B 91 ASP B 209 NAP B 303 SITE 2 AC7 5 HOH B 439 SITE 1 AC8 6 GLU B 70 ASP B 88 ILE B 90 NAP B 303 SITE 2 AC8 6 HOH B 418 HOH B 423 SITE 1 AC9 28 SER A 178 ARG A 180 GLU B 70 ASP B 88 SITE 2 AC9 28 ILE B 90 ASP B 91 GLY B 92 THR B 93 SITE 3 AC9 28 ALA B 94 ASN B 160 VAL B 163 GLY B 183 SITE 4 AC9 28 CYS B 185 ASN B 202 THR B 203 ASN B 204 SITE 5 AC9 28 ASP B 209 CA B 301 CA B 302 HOH B 403 SITE 6 AC9 28 HOH B 404 HOH B 407 HOH B 411 HOH B 413 SITE 7 AC9 28 HOH B 419 HOH B 420 HOH B 423 HOH B 434 CRYST1 64.505 60.331 79.939 90.00 108.28 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 0.015503 0.000000 0.005121 0.00000 SCALE2 0.000000 0.016575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013174 0.00000