HEADER TRANSFERASE 05-SEP-13 4MKG TITLE CRYSTAL STRUCTURE OF A STABLE ADENYLATE KINASE VARIANT AKV8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AK, ATP-AMP TRANSPHOSPHORYLASE, ATP:AMP PHOSPHOTRANSFERASE, COMPND 5 ADENYLATE MONOPHOSPHATE KINASE, SUPEROXIDE-INDUCIBLE PROTEIN 16, COMPND 6 SOI16; COMPND 7 EC: 2.7.4.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: ADK, BSU01370; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ADENYLATE KINASE, ZINC FINGER, TRANSFERASE ACTIVITY, KEYWDS 2 PHOSPHOTRANSFERASE ACTIVITY, ZINC BINDING, ATP BINDING, KEYWDS 3 PHOSPHORYLATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MOON,D.JUNG,E.BAE REVDAT 3 08-NOV-23 4MKG 1 REMARK REVDAT 2 24-AUG-22 4MKG 1 JRNL REMARK SEQADV LINK REVDAT 1 26-MAR-14 4MKG 0 JRNL AUTH S.MOON,D.K.JUNG,G.N.PHILLIPS JR.,E.BAE JRNL TITL AN INTEGRATED APPROACH FOR THERMAL STABILIZATION OF A JRNL TITL 2 MESOPHILIC ADENYLATE KINASE. JRNL REF PROTEINS V. 82 1947 2014 JRNL REFN ESSN 1097-0134 JRNL PMID 24615904 JRNL DOI 10.1002/PROT.24549 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43604 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2187 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2828 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1688 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.79000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.062 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.186 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 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): 1773 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2406 ; 2.564 ; 2.036 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 216 ; 5.848 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;35.509 ;25.190 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 321 ;13.770 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.386 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 270 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1304 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 31 A 60 REMARK 3 ORIGIN FOR THE GROUP (A): 21.3663 -3.1770 9.0579 REMARK 3 T TENSOR REMARK 3 T11: 0.2726 T22: 0.0856 REMARK 3 T33: 0.3940 T12: 0.1182 REMARK 3 T13: 0.2963 T23: 0.0980 REMARK 3 L TENSOR REMARK 3 L11: 4.0352 L22: 3.5648 REMARK 3 L33: 4.6643 L12: 0.4174 REMARK 3 L13: -0.7413 L23: -2.0929 REMARK 3 S TENSOR REMARK 3 S11: -0.4933 S12: 0.0461 S13: -0.7539 REMARK 3 S21: -0.7397 S22: -0.3367 S23: -0.7653 REMARK 3 S31: 0.8944 S32: 0.4095 S33: 0.8300 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 : A 127 A 164 REMARK 3 ORIGIN FOR THE GROUP (A): 1.7312 -7.0213 14.4507 REMARK 3 T TENSOR REMARK 3 T11: 0.1727 T22: 0.0422 REMARK 3 T33: 0.0591 T12: -0.0096 REMARK 3 T13: 0.0633 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 2.1005 L22: 3.2574 REMARK 3 L33: 1.3096 L12: 1.3368 REMARK 3 L13: -0.6202 L23: -1.1681 REMARK 3 S TENSOR REMARK 3 S11: -0.1816 S12: 0.1824 S13: -0.1188 REMARK 3 S21: -0.4755 S22: 0.1028 S23: -0.0856 REMARK 3 S31: 0.3376 S32: -0.0888 S33: 0.0788 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 30 REMARK 3 RESIDUE RANGE : A 61 A 126 REMARK 3 RESIDUE RANGE : A 165 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1063 12.0400 13.8419 REMARK 3 T TENSOR REMARK 3 T11: 0.0220 T22: 0.0420 REMARK 3 T33: 0.0405 T12: 0.0118 REMARK 3 T13: 0.0047 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 1.1336 L22: 1.0549 REMARK 3 L33: 1.1550 L12: 0.4805 REMARK 3 L13: -0.6873 L23: -0.5099 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: -0.0739 S13: -0.0636 REMARK 3 S21: 0.0305 S22: -0.0461 S23: -0.0820 REMARK 3 S31: -0.0119 S32: 0.1030 S33: 0.0767 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): 10.3992 2.2948 16.9717 REMARK 3 T TENSOR REMARK 3 T11: 0.1175 T22: 0.1044 REMARK 3 T33: 0.1622 T12: 0.0285 REMARK 3 T13: 0.0541 T23: 0.0465 REMARK 3 L TENSOR REMARK 3 L11: 2.1459 L22: 3.7220 REMARK 3 L33: 1.9428 L12: 2.7374 REMARK 3 L13: -1.8444 L23: -2.0773 REMARK 3 S TENSOR REMARK 3 S11: -0.2096 S12: -0.1237 S13: -0.3812 REMARK 3 S21: -0.1412 S22: -0.1666 S23: -0.4087 REMARK 3 S31: 0.2973 S32: 0.1166 S33: 0.3762 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4MKG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DCM SI (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : IMOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 44.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 <I/SIGMA(I)> 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: 1P3J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M TRISODIUM CITRATE PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K, PH 7.0 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 22.31000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.99500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.66000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.99500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.31000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.66000 REMARK 290 SMTRY3 4 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: 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 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 662 O HOH A 684 2.01 REMARK 500 O HOH A 513 O HOH A 530 2.06 REMARK 500 O HOH A 668 O HOH A 704 2.15 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 HIS A 138 CG HIS A 138 CD2 0.075 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 MET A 1 CG - SD - CE ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG A 19 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = 8.9 DEGREES REMARK 500 ASP A 33 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 71 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 76 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = -7.7 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = -10.1 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = 7.4 DEGREES REMARK 500 LEU A 182 CA - CB - CG ANGL. DEV. = 16.4 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 ASN A 142 67.65 -165.28 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 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 CYS A 133 SG 109.9 REMARK 620 3 CYS A 150 SG 103.5 113.8 REMARK 620 4 ASP A 153 OD2 114.7 100.7 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A 303 O2G REMARK 620 2 AP5 A 303 O2B 82.7 REMARK 620 3 HOH A 412 O 91.0 84.0 REMARK 620 4 HOH A 434 O 97.3 94.3 171.2 REMARK 620 5 HOH A 439 O 159.8 117.3 88.7 84.4 REMARK 620 6 HOH A 445 O 87.5 169.7 99.4 83.7 72.6 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 ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MKF RELATED DB: PDB REMARK 900 RELATED ID: 4MKH RELATED DB: PDB DBREF 4MKG A 1 217 UNP P16304 KAD_BACSU 1 217 SEQADV 4MKG ILE A 3 UNP P16304 LEU 3 ENGINEERED MUTATION SEQADV 4MKG ALA A 17 UNP P16304 GLY 17 ENGINEERED MUTATION SEQADV 4MKG LYS A 23 UNP P16304 ASP 23 ENGINEERED MUTATION SEQADV 4MKG ARG A 69 UNP P16304 LYS 69 ENGINEERED MUTATION SEQADV 4MKG SER A 73 UNP P16304 GLY 73 ENGINEERED MUTATION SEQADV 4MKG SER A 75 UNP P16304 ASP 75 ENGINEERED MUTATION SEQADV 4MKG MET A 103 UNP P16304 TYR 103 ENGINEERED MUTATION SEQADV 4MKG ARG A 105 UNP P16304 LYS 105 ENGINEERED MUTATION SEQADV 4MKG GLN A 114 UNP P16304 GLU 114 ENGINEERED MUTATION SEQADV 4MKG GLU A 118 UNP P16304 ASP 118 ENGINEERED MUTATION SEQADV 4MKG GLU A 119 UNP P16304 VAL 119 ENGINEERED MUTATION SEQADV 4MKG THR A 169 UNP P16304 SER 169 ENGINEERED MUTATION SEQADV 4MKG ALA A 180 UNP P16304 GLN 180 ENGINEERED MUTATION SEQADV 4MKG ALA A 184 UNP P16304 ASP 184 ENGINEERED MUTATION SEQADV 4MKG ASP A 187 UNP P16304 SER 187 ENGINEERED MUTATION SEQADV 4MKG SER A 188 UNP P16304 GLU 188 ENGINEERED MUTATION SEQADV 4MKG GLU A 190 UNP P16304 GLY 190 ENGINEERED MUTATION SEQADV 4MKG VAL A 191 UNP P16304 TYR 191 ENGINEERED MUTATION SEQADV 4MKG VAL A 193 UNP P16304 ALA 193 ENGINEERED MUTATION SEQADV 4MKG PHE A 205 UNP P16304 TYR 205 ENGINEERED MUTATION SEQADV 4MKG VAL A 210 UNP P16304 ASP 210 ENGINEERED MUTATION SEQADV 4MKG ILE A 211 UNP P16304 LEU 211 ENGINEERED MUTATION SEQADV 4MKG GLN A 217 UNP P16304 LYS 217 ENGINEERED MUTATION SEQRES 1 A 217 MET ASN ILE VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 217 GLY THR GLN ALA GLU ARG ILE VAL GLU LYS TYR GLY ILE SEQRES 3 A 217 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 A 217 LYS GLU GLU THR PRO LEU GLY LEU GLU ALA LYS SER TYR SEQRES 5 A 217 ILE ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 217 GLY ILE VAL ARG GLU ARG LEU SER LYS SER ASP CYS GLU SEQRES 7 A 217 ARG GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 217 GLN ALA GLU ALA LEU GLU GLU ILE LEU GLU GLU MET GLY SEQRES 9 A 217 ARG PRO ILE ASP TYR VAL ILE ASN ILE GLN VAL ASP LYS SEQRES 10 A 217 GLU GLU LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 217 SER VAL CYS GLY THR THR TYR HIS LEU VAL PHE ASN PRO SEQRES 12 A 217 PRO LYS THR PRO GLY ILE CYS ASP LYS ASP GLY GLY GLU SEQRES 13 A 217 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL THR SEQRES 14 A 217 LYS ARG LEU GLU VAL ASN MET LYS GLN THR ALA PRO LEU SEQRES 15 A 217 LEU ALA PHE TYR ASP SER LYS GLU VAL LEU VAL ASN VAL SEQRES 16 A 217 ASN GLY GLN GLN ASP ILE GLN ASP VAL PHE ALA ASP VAL SEQRES 17 A 217 LYS VAL ILE LEU GLY GLY LEU LYS GLN HET ZN A 301 1 HET MG A 302 1 HET AP5 A 303 57 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 AP5 C20 H29 N10 O22 P5 FORMUL 5 HOH *321(H2 O) HELIX 1 1 GLY A 12 GLY A 25 1 14 HELIX 2 2 THR A 31 GLU A 42 1 12 HELIX 3 3 THR A 43 LYS A 55 1 13 HELIX 4 4 PRO A 60 SER A 73 1 14 HELIX 5 5 LYS A 74 GLY A 80 5 7 HELIX 6 6 THR A 89 GLY A 104 1 16 HELIX 7 7 ASP A 116 GLY A 126 1 11 HELIX 8 8 ARG A 160 ASP A 163 5 4 HELIX 9 9 ASN A 164 LYS A 189 1 26 HELIX 10 10 ASP A 200 GLY A 214 1 15 SHEET 1 A 5 HIS A 28 SER A 30 0 SHEET 2 A 5 PHE A 81 ASP A 84 1 O LEU A 82 N ILE A 29 SHEET 3 A 5 ASN A 2 MET A 6 1 N ILE A 3 O PHE A 81 SHEET 4 A 5 TYR A 109 GLN A 114 1 O ILE A 111 N VAL A 4 SHEET 5 A 5 LEU A 192 ASN A 196 1 O VAL A 195 N GLN A 114 SHEET 1 B 3 THR A 136 HIS A 138 0 SHEET 2 B 3 ARG A 127 CYS A 130 -1 N ARG A 128 O TYR A 137 SHEET 3 B 3 LEU A 157 TYR A 158 -1 O TYR A 158 N ILE A 129 LINK SG CYS A 130 ZN ZN A 301 1555 1555 2.38 LINK SG CYS A 133 ZN ZN A 301 1555 1555 2.28 LINK SG CYS A 150 ZN ZN A 301 1555 1555 2.37 LINK OD2 ASP A 153 ZN ZN A 301 1555 1555 2.06 LINK MG MG A 302 O2G AP5 A 303 1555 1555 2.29 LINK MG MG A 302 O2B AP5 A 303 1555 1555 2.34 LINK MG MG A 302 O HOH A 412 1555 1555 2.51 LINK MG MG A 302 O HOH A 434 1555 1555 2.40 LINK MG MG A 302 O HOH A 439 1555 1555 2.34 LINK MG MG A 302 O HOH A 445 1555 1555 2.49 CISPEP 1 PHE A 86 PRO A 87 0 -6.57 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 ASP A 153 SITE 1 AC2 5 AP5 A 303 HOH A 412 HOH A 434 HOH A 439 SITE 2 AC2 5 HOH A 445 SITE 1 AC3 41 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC3 41 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC3 41 GLY A 32 PHE A 35 ARG A 36 ILE A 53 SITE 4 AC3 41 GLU A 57 VAL A 59 THR A 64 GLY A 85 SITE 5 AC3 41 PHE A 86 ARG A 88 GLN A 92 ARG A 123 SITE 6 AC3 41 ARG A 127 THR A 136 TYR A 137 HIS A 138 SITE 7 AC3 41 PHE A 141 ARG A 160 ARG A 171 GLN A 199 SITE 8 AC3 41 ILE A 201 MG A 302 HOH A 404 HOH A 412 SITE 9 AC3 41 HOH A 414 HOH A 417 HOH A 419 HOH A 434 SITE 10 AC3 41 HOH A 445 HOH A 451 HOH A 456 HOH A 471 SITE 11 AC3 41 HOH A 688 CRYST1 44.620 61.320 87.990 90.00 90.00 90.00 P 21 21 21 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 0.022411 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011365 0.00000