HEADER TRANSFERASE 26-JUN-08 3DL0 TITLE CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ATP-AMP TRANSPHOSPHORYLASE, AK, SUPEROXIDE-INDUCIBLE PROTEIN COMPND 5 16, SOI16; COMPND 6 EC: 2.7.4.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: ADK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS PHOSPHOTRANSFERASE, ZINC COORDINATION, ATP-BINDING, KINASE, METAL- KEYWDS 2 BINDING, NUCLEOTIDE BIOSYNTHESIS, NUCLEOTIDE-BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.BANNEN,C.M.BIANCHETTI,C.A.BINGMAN,J.G.MCCOY REVDAT 6 30-AUG-23 3DL0 1 REMARK LINK REVDAT 5 25-OCT-17 3DL0 1 REMARK REVDAT 4 15-OCT-14 3DL0 1 JRNL REVDAT 3 25-JUN-14 3DL0 1 JRNL REVDAT 2 24-OCT-12 3DL0 1 VERSN REVDAT 1 09-JUN-09 3DL0 0 JRNL AUTH S.MOON,R.M.BANNEN,T.J.RUTKOSKI,G.N.PHILLIPS,E.BAE JRNL TITL EFFECTIVENESS AND LIMITATIONS OF LOCAL STRUCTURAL ENTROPY JRNL TITL 2 OPTIMIZATION IN THE THERMAL STABILIZATION OF MESOPHILIC AND JRNL TITL 3 THERMOPHILIC ADENYLATE KINASES. JRNL REF PROTEINS V. 82 2631 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 24931334 JRNL DOI 10.1002/PROT.24627 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54455 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2758 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3741 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 118 REMARK 3 SOLVENT ATOMS : 535 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : 0.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.038 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3581 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4873 ; 1.508 ; 2.047 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 448 ; 5.318 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;35.705 ;25.570 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 655 ;13.704 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.787 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2634 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1800 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2472 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 431 ; 0.144 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.019 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 77 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 63 ; 0.220 ; 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): 2217 ; 0.833 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3493 ; 1.293 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1526 ; 2.064 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1371 ; 3.201 ; 4.500 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 : 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 REMARK 4 REMARK 4 3DL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59416 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3DKV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG MME 2000, 100MM NACL, 100MM REMARK 280 HEPPS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 38.34400 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 221 O HOH B 496 2656 1.63 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 64.91 -159.09 REMARK 500 ASP A 163 36.03 -94.17 REMARK 500 ASN B 142 65.69 -154.24 REMARK 500 ASP B 163 48.91 -94.03 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 219 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 CYS A 133 SG 110.4 REMARK 620 3 CYS A 150 SG 107.9 106.6 REMARK 620 4 ASP A 153 OD1 108.9 122.8 98.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 220 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A 218 O2B REMARK 620 2 AP5 A 218 O2G 75.9 REMARK 620 3 HOH A 225 O 85.7 90.6 REMARK 620 4 HOH A 231 O 113.2 166.1 80.0 REMARK 620 5 HOH A 241 O 158.2 84.0 86.3 85.2 REMARK 620 6 HOH A 460 O 83.9 97.3 164.9 94.2 107.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 219 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 130 SG REMARK 620 2 CYS B 133 SG 110.8 REMARK 620 3 CYS B 150 SG 108.7 105.3 REMARK 620 4 ASP B 153 OD1 110.4 123.1 96.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 220 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 B 218 O2B REMARK 620 2 AP5 B 218 O2G 75.3 REMARK 620 3 HOH B 226 O 165.6 90.5 REMARK 620 4 HOH B 231 O 87.4 102.7 97.6 REMARK 620 5 HOH B 254 O 109.8 174.3 84.6 75.2 REMARK 620 6 HOH B 499 O 79.9 91.0 98.9 158.5 92.7 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 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 B 218 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DKV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE GENE WAS SYNTHESIZED BY DE NOVO SYNTHESIS. MUTATIONS REMARK 999 WERE MADE TO AN ADENYLATE KINASE SEQUENCE FROM BACILLUS REMARK 999 SUBTILIS TO OPTIMIZE THE PROTEIN'S STRUCTURAL ENTROPY. DBREF 3DL0 A 1 216 UNP P16304 KAD_BACSU 1 216 DBREF 3DL0 B 1 216 UNP P16304 KAD_BACSU 1 216 SEQADV 3DL0 LYS A 23 UNP P16304 ASP 23 SEE REMARK 999 SEQADV 3DL0 MET A 103 UNP P16304 TYR 103 SEE REMARK 999 SEQADV 3DL0 GLN A 114 UNP P16304 GLU 114 SEE REMARK 999 SEQADV 3DL0 THR A 169 UNP P16304 SER 169 SEE REMARK 999 SEQADV 3DL0 ALA A 180 UNP P16304 GLN 180 SEE REMARK 999 SEQADV 3DL0 ASP A 187 UNP P16304 SER 187 SEE REMARK 999 SEQADV 3DL0 VAL A 193 UNP P16304 ALA 193 SEE REMARK 999 SEQADV 3DL0 LEU A 208 UNP P16304 VAL 208 SEE REMARK 999 SEQADV 3DL0 VAL A 210 UNP P16304 ASP 210 SEE REMARK 999 SEQADV 3DL0 LYS B 23 UNP P16304 ASP 23 SEE REMARK 999 SEQADV 3DL0 MET B 103 UNP P16304 TYR 103 SEE REMARK 999 SEQADV 3DL0 GLN B 114 UNP P16304 GLU 114 SEE REMARK 999 SEQADV 3DL0 THR B 169 UNP P16304 SER 169 SEE REMARK 999 SEQADV 3DL0 ALA B 180 UNP P16304 GLN 180 SEE REMARK 999 SEQADV 3DL0 ASP B 187 UNP P16304 SER 187 SEE REMARK 999 SEQADV 3DL0 VAL B 193 UNP P16304 ALA 193 SEE REMARK 999 SEQADV 3DL0 LEU B 208 UNP P16304 VAL 208 SEE REMARK 999 SEQADV 3DL0 VAL B 210 UNP P16304 ASP 210 SEE REMARK 999 SEQRES 1 A 216 MET ASN LEU VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 216 GLY THR GLN GLY GLU ARG ILE VAL GLU LYS TYR GLY ILE SEQRES 3 A 216 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 A 216 LYS GLU GLU THR PRO LEU GLY LEU GLU ALA LYS SER TYR SEQRES 5 A 216 ILE ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 216 GLY ILE VAL LYS GLU ARG LEU GLY LYS ASP ASP CYS GLU SEQRES 7 A 216 ARG GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 216 GLN ALA GLU ALA LEU GLU GLU ILE LEU GLU GLU MET GLY SEQRES 9 A 216 LYS PRO ILE ASP TYR VAL ILE ASN ILE GLN VAL ASP LYS SEQRES 10 A 216 ASP VAL LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 216 SER VAL CYS GLY THR THR TYR HIS LEU VAL PHE ASN PRO SEQRES 12 A 216 PRO LYS THR PRO GLY ILE CYS ASP LYS ASP GLY GLY GLU SEQRES 13 A 216 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL THR SEQRES 14 A 216 LYS ARG LEU GLU VAL ASN MET LYS GLN THR ALA PRO LEU SEQRES 15 A 216 LEU ASP PHE TYR ASP GLU LYS GLY TYR LEU VAL ASN VAL SEQRES 16 A 216 ASN GLY GLN GLN ASP ILE GLN ASP VAL TYR ALA ASP LEU SEQRES 17 A 216 LYS VAL LEU LEU GLY GLY LEU LYS SEQRES 1 B 216 MET ASN LEU VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 B 216 GLY THR GLN GLY GLU ARG ILE VAL GLU LYS TYR GLY ILE SEQRES 3 B 216 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 B 216 LYS GLU GLU THR PRO LEU GLY LEU GLU ALA LYS SER TYR SEQRES 5 B 216 ILE ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 B 216 GLY ILE VAL LYS GLU ARG LEU GLY LYS ASP ASP CYS GLU SEQRES 7 B 216 ARG GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 B 216 GLN ALA GLU ALA LEU GLU GLU ILE LEU GLU GLU MET GLY SEQRES 9 B 216 LYS PRO ILE ASP TYR VAL ILE ASN ILE GLN VAL ASP LYS SEQRES 10 B 216 ASP VAL LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 B 216 SER VAL CYS GLY THR THR TYR HIS LEU VAL PHE ASN PRO SEQRES 12 B 216 PRO LYS THR PRO GLY ILE CYS ASP LYS ASP GLY GLY GLU SEQRES 13 B 216 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL THR SEQRES 14 B 216 LYS ARG LEU GLU VAL ASN MET LYS GLN THR ALA PRO LEU SEQRES 15 B 216 LEU ASP PHE TYR ASP GLU LYS GLY TYR LEU VAL ASN VAL SEQRES 16 B 216 ASN GLY GLN GLN ASP ILE GLN ASP VAL TYR ALA ASP LEU SEQRES 17 B 216 LYS VAL LEU LEU GLY GLY LEU LYS HET ZN A 219 1 HET MG A 220 1 HET AP5 A 218 57 HET ZN B 219 1 HET MG B 220 1 HET AP5 B 218 57 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE FORMUL 3 ZN 2(ZN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 5 AP5 2(C20 H29 N10 O22 P5) FORMUL 9 HOH *535(H2 O) HELIX 1 1 GLY A 12 TYR A 24 1 13 HELIX 2 2 THR A 31 GLU A 41 1 11 HELIX 3 3 THR A 43 ASP A 54 1 12 HELIX 4 4 PRO A 60 GLY A 73 1 14 HELIX 5 5 LYS A 74 GLU A 78 5 5 HELIX 6 6 THR A 89 MET A 103 1 15 HELIX 7 7 ASP A 116 ASP A 118 5 3 HELIX 8 8 VAL A 119 GLY A 126 1 8 HELIX 9 9 ASN A 164 GLY A 190 1 27 HELIX 10 10 ASP A 200 GLY A 213 1 14 HELIX 11 11 GLY A 214 LYS A 216 5 3 HELIX 12 12 GLY B 12 TYR B 24 1 13 HELIX 13 13 THR B 31 GLU B 42 1 12 HELIX 14 14 THR B 43 GLY B 56 1 14 HELIX 15 15 PRO B 60 GLY B 73 1 14 HELIX 16 16 LYS B 74 GLU B 78 5 5 HELIX 17 17 THR B 89 GLY B 104 1 16 HELIX 18 18 ASP B 116 ASP B 118 5 3 HELIX 19 19 VAL B 119 GLY B 126 1 8 HELIX 20 20 ASN B 164 GLY B 190 1 27 HELIX 21 21 ASP B 200 GLY B 213 1 14 HELIX 22 22 GLY B 214 LYS B 216 5 3 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 LEU A 5 O LEU A 83 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 193 N VAL A 110 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 SHEET 1 C 5 HIS B 28 SER B 30 0 SHEET 2 C 5 PHE B 81 ASP B 84 1 O LEU B 82 N ILE B 29 SHEET 3 C 5 ASN B 2 MET B 6 1 N LEU B 5 O LEU B 83 SHEET 4 C 5 TYR B 109 GLN B 114 1 O ILE B 111 N VAL B 4 SHEET 5 C 5 LEU B 192 ASN B 196 1 O VAL B 193 N ASN B 112 SHEET 1 D 3 THR B 136 HIS B 138 0 SHEET 2 D 3 ARG B 127 CYS B 130 -1 N ARG B 128 O TYR B 137 SHEET 3 D 3 LEU B 157 TYR B 158 -1 O TYR B 158 N ILE B 129 LINK SG CYS A 130 ZN ZN A 219 1555 1555 2.32 LINK SG CYS A 133 ZN ZN A 219 1555 1555 2.34 LINK SG CYS A 150 ZN ZN A 219 1555 1555 2.36 LINK OD1 ASP A 153 ZN ZN A 219 1555 1555 2.07 LINK O2B AP5 A 218 MG MG A 220 1555 1555 2.37 LINK O2G AP5 A 218 MG MG A 220 1555 1555 2.37 LINK MG MG A 220 O HOH A 225 1555 1555 2.60 LINK MG MG A 220 O HOH A 231 1555 1555 2.19 LINK MG MG A 220 O HOH A 241 1555 1555 2.43 LINK MG MG A 220 O HOH A 460 1555 1555 2.18 LINK SG CYS B 130 ZN ZN B 219 1555 1555 2.28 LINK SG CYS B 133 ZN ZN B 219 1555 1555 2.34 LINK SG CYS B 150 ZN ZN B 219 1555 1555 2.33 LINK OD1 ASP B 153 ZN ZN B 219 1555 1555 2.00 LINK O2B AP5 B 218 MG MG B 220 1555 1555 2.36 LINK O2G AP5 B 218 MG MG B 220 1555 1555 2.29 LINK MG MG B 220 O HOH B 226 1555 1555 2.32 LINK MG MG B 220 O HOH B 231 1555 1555 2.63 LINK MG MG B 220 O HOH B 254 1555 1555 2.28 LINK MG MG B 220 O HOH B 499 1555 1555 2.29 CISPEP 1 PHE A 86 PRO A 87 0 -7.66 CISPEP 2 PHE B 86 PRO B 87 0 -5.30 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 ASP A 153 SITE 1 AC2 4 CYS B 130 CYS B 133 CYS B 150 ASP B 153 SITE 1 AC5 27 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC5 27 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC5 27 GLY A 32 ARG A 36 ILE A 53 GLU A 57 SITE 4 AC5 27 THR A 64 GLY A 85 PHE A 86 ARG A 88 SITE 5 AC5 27 GLN A 92 ARG A 123 LEU A 124 ARG A 127 SITE 6 AC5 27 TYR A 137 HIS A 138 PHE A 141 ARG A 160 SITE 7 AC5 27 ARG A 171 GLN A 199 ILE A 201 SITE 1 AC6 28 PRO B 9 GLY B 10 ALA B 11 GLY B 12 SITE 2 AC6 28 LYS B 13 GLY B 14 THR B 15 THR B 31 SITE 3 AC6 28 GLY B 32 PHE B 35 ARG B 36 ILE B 53 SITE 4 AC6 28 GLU B 57 THR B 64 GLY B 85 PHE B 86 SITE 5 AC6 28 ARG B 88 GLN B 92 ARG B 123 LEU B 124 SITE 6 AC6 28 ARG B 127 TYR B 137 HIS B 138 PHE B 141 SITE 7 AC6 28 ARG B 160 ARG B 171 GLN B 199 ILE B 201 CRYST1 34.003 76.688 77.993 90.00 95.30 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 0.029409 0.000000 0.002729 0.00000 SCALE2 0.000000 0.013040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012877 0.00000